His physical attacks do give more damage than any of his spells do as a boss. It's mostly his human form that's not a physical fighter, his Heaven and Hell forms are adept in both. Palamecia's destruction did 0 damage to the Emperor. And withstood hits from Ultima, which should be much stronger than Flare or Holy.
Exact percentage randomizer, probably game mechanics yes, but so is the weakness mentioned on his profile. But still he does heal health really fast and striking attacks are really potent. Emperor in Hell form, was a great challenge for the combined power of
Firio,
Maria,
Guy, and
Leo; all of which are
5-C individually and should each be stronger in terms of AP and Durability than the 32 Exaton feat. Heaven form was also the greatest challenge to the combined strength of Minwu, Scott, Joseph, and Ricard; who fought against
Ultima Weapo. Might be an outlier given Dissidia's inconsistencies however; but Everlasting has plans for really big Final Fantasy revisions.
Never used BFR, I addressed it's OoC for him. But he still regularly uses teleportation to dodge attacks in Dissidia iirc; note that Dissidia is canon. Also, actually Mateus uses Time Slow and Haste in battle regularly.
His dual existence as the Light and Dark Emperor makes him difficult to kill. Basically, he switches forms each time he "Dies".
Can exist in two places at the same time (Heaven and Hell), I guess that sounds more like Spatial Intangibility than it does resurrection.