I fundamentally disagree with Dragon Emperor. Reading the Type Moon Wiki, which is a REALLY good source, I see 0 information that corroborates his statement, leading me to believe that's an interpretation alone based on the way he phrases it. Not only that, but it doesn't even negate any of the extenuating issues with Zekka's nature.
"Magecraft (Ú¡öÞíô, Majutsu?), or Thaumaturgy, is the artificial reenactment of Mystery, which is ordinarily possible only by inhuman beings.[1][2]
It is the ability to bring about what is possible through science with supernatural means; although the process is considered a miracle, the result is not. The limits of Magecraft have changed with time, as science evolved and Magic from the past became possible through science."
I mean, you can literally just read the Type Moon wiki— don't. Actually. It's a LOT of information to digest.
So, from this information, I would say a few things.
1. Zekka's vibration attacks are explained by martial artists who state nothing mystical about his abilities. Almost everything else about everything in the verse is related to soft science fiction concepts. Things like Don Fua's Black hole attacks and Zekka's antimatter strikes delve into and are brought about using some sort of sci-fi bullshit, so to argue that he might be "magical" in a verse that has nothing to support that claim whatsoever just because not every single breath he takes has a paragraph and translators note to justify his bullshit is rather weak. In addition, this is coming from a verse that uses its soft sci-fi in notes to explain things that happen in the story with small paragraphs in the margins. To substantiate the claim that Zekka is mystical, you would need more evidence than the fact that not every single page has a 20 paragraph essay on his machinery specs. Even concepts that would otherwise be totally unbelievable are reduced to technology. Don Fua can fade in between dimensions through the use of a special device in his body according to Trinidad, who can **** people's bodies up using his connection to cyberspace thanks to the 3 chips in his brain.
So, a lot of it is rather explained by "science".
2. The definition of magecraft applies mystery to things, and it has nothing to do with it being "unknowable"— more that Mystery is a word for magical quality. It by definition doesn't break the laws of what is possible in the universe because it's essentially preforming possible things without the necessary technology, having magic energy as the catalyst. Zekka's body is literally a scientific machine, designed to do a whole bunch of the shit that he does. He himself put in an antimatter reactor that gave him his suicide move, and Sech's body was built for fighting it seems, or at least given to him with the purpose to defeat Zekka in mind, making it a modern weapon. Worse, Zekka is the same type of body as Sechs, and he's dedicated every moment of his existence it seems to being a manifestation of Karate itself. He's as "weapon" and "modern" as it gets. Arguably taken to the highest degree in both based on him being a futuristic killing machine, even if that path was chosen by him.
3. The argument that Ghosts are without quality of mystery directly contradicts what is considered "supernatural" by fate, which, and I don't mean to be rude, discredits your opinion in my eyes, because that's not how the verse works in the most obvious ways. By that logic, Servants, which are able to be reduced to time traveling ghosts, aren't "mysterious" either.
4. A person with enough brute strength to level a continent would definitely have to have Mystery if they were a native to type moon, but the problem is...
A. Zekka isn't a person. He would not have a soul, given everything including his mind is synthetic. Even Gally wondered if she, in her artificial existence, had a soul. And by our standards, robots don't have souls. He's more a robot suit of armor controlled by a remote system, or a Gundam than a person, and Gundams won't hurt servants, no matter how strong they are, especially if they are BUILT to be that powerful. Which, for all intents and purposes, cyborgs in Gunnm... Are...? I don't think you can train a robotic body even in this verse— you likely improve your skill by improving your body's technology and how you use it, which is consistent in many parts of the verse, and even Gally's body and Sechs whole existence was built with fighting and in Gally's case, adapting in combat, in mind. The argument that he can be seen as a weapon is way stronger than him being seen as a "mystery" infused metal golem that lacks a soul to be considered a real golem or any form of magic thing...? The main arguments are basically "he's strong, and from an anime where you can do crazy shit". Not even shitty old 1800s guns can hurt them unless used by other servants. Drake's guns are old and primitive, but they work because they're magic.
B. A flesh and blood person isn't affected by this phenomena anyway, so a 3A fleshy boi with nothing else besides AP can still hurt a servant. Normal people and magus are too weak to accomplish dealing any real damage to them because they have, like, no AP to hurt them. Not because they're naturally immune, nor because they have some sort of magic energy surrounding all of their attacks. Unless you wanna upgrade them to be immune to non-magical damage or something, which I disagree with I think? Point is, them being continent level would help them hurt a servant anyway. They never had a problem touching them because of this immunity.
C. In Type Moon, you cant be strong without having Mystery. So, to claim that anyone strong in any other verse has Mystery by virtue of being strong is not a rational argument. Sure, everyone in Type Moon who is strong is therefore filled with Mystery because otherwise strength on that level is impossible, but not everyone outside of Type Moon applies to that obviously. It's a verse specific thing, and in order for us to judge whether or not other verses meet the requirement, they have to have something similar. Like magic. Or specifically mutant or psychic powers. Zekka doesn't even have any "superpowers" considering he's a robot. All of it is just functions and things that are built into him or his robotic body is exploited by him using its natural functions to his advantage.
Overall... Nah.
We can ignore that immunity for sake of conversation, but that means 2 things.
1. We need to note it in the OP.
2. It cannot he added to pages for obvious reasons.
Edit: Also. Again. Ghosts are magic in Type Moon. Or... "Mystery"
"If it is believed that the subject of a Mystery "exists," the World permits its existence. Definite affirmation of said belief is not required, so even though the majority of modern humans reject the existence of ghosts, modern science cannot outright demonstrate that they do not exist, and, thus, within the unconscious, there lurks the vague suspicion that "they might indeed exist." This sort of "suspicion" falls under the category of "faith." "Ignorance" is the force that opposes "faith". If the existence of ghosts is itself utterly unknown, faith cannot foment."
Then, if you look on the wiki for Wraiths and Ghosts, you would find this; "Wraith (õ║íÚ£è, Bourei?), also referred to as Ghosts (Õ╣¢Ú£è, Yürei?) or Human spirits, are souls of dead people that remain attached to this world due to past grudges, regrets and other sorts of unfinished business that they had during life. As such, they tend to haunt places, items or people that are related to their unfinished business."
Ghosts are Mysteries.
Also, his explosion punch is theoretically (using that word loosely) possible, just as being able to kick off of the air and double jump is "theoretically" possible. That's not... Magic. And it's definitely not enough to justify applying something to him just because you think "Mystery" = Cool impossible shit that lacks explanation. When I am certain that's not the case. Unless someone's gonna debunk the entire Type Moon wiki and more importantly, the actual parts I am referring to.
So, like, no. This is more like you're making appeals to a vague definition using flimsy justifications than an actual argument with valid points.