The universe contains the afterlife and mortal universe. The former seemingly doesn't have time or it at least flows differently, while the latter is the same as a normal universe. The kaioshin realm exists outside of all that, even though they are all in the universal bubble. How does an attack that trascends the space-time of one universe to get to another not equate to space-time being destroyed, regardless of if only one has such properties?
Goku in Z says
time flows differently in the afterlife, which means for Zeno to have erased an entire universe, he'd have to transcend the time space of the mortal universe to reach the afterlife/demon realm, and the Supreme Kai realm that resides outside of the universe given the DB map.
In addition to that, we see Infinite Zamasu
beginning to creep through the
distortio in time and space that Trunks created with his time machine (he never made it completely through), validated by Pilaf and crew standing in front of the void watching it, and Beerus and Whis feeling his energy, meaning Zeno also destroyed Zamasu who was connected to all of the Universe's time and space.
The reason I bring this up is because Beerus and Goku were hitting each other with blows that could
destroy the universe,
turning it into a void . Zeno turned future U7 into a void, and Zamasu gives evidence that he was attached to space time as well, and Zeno erased him.
Scaling-wise, this would make a lot of characters Low 2-C.
destroy the universe, turning it into a void
"Destroying the very universe"
"Their super power threatened to annihilate the universe itself"
"That power is capable of destroying the universe"
"It will turn into a vacuum made of nothingness"
"Power capable of destroying even the universe itself"
So, overwhelming evidence clearly shows the entire universe itself would be destroyed, not it's contents. There was evidence of Zamasu attempting to travel through a distortion in space-time, which among the statements of Zamasu literally becoming the universe, is evidence of the destruction of time and space.
Zamasu became the universe itself, and Zeno destroyed him, turning it into a void.
Elder Kai stated
multiple times that the universe itself would be destroyed, with one statement saying it will be turned into a vacuum of nothingness.
So unless we're comparing two different works of fiction, I don't see how they're different.