Well,
"Who would...?" is simply a rhetorical question of astonishment and bewilderment, not a literal expression of confusion over who was responsible for ripping out the Jenova specimen from the container it was in. Sephiroth was there, she saw him. Now she's seeing a bloody alien container busted from the outside with part of the specimens guts pulled out.
Detectives and crime scene investigators gasp in shock upon witnessing a gruesome enough bloodbath and what do they usually say? "Who would do such a thing?" when clearly, the
murderer would, since... This
is their mess. It's a shock of sensibilities, not being able to conceptualize someone doing an act so bizarre and violent. Your examples apparently don't leave room for Tifa to simply be shocked and bewildered by seeing a supposed dead supersoldier suddenly blink into existence, cut a bridge they were standing on and then suddenly confiscate an alien for no discernable reason.
Rhetorical questions meant to point out details aren't that strange. Tifa being shocked at the bizarre alien blood bath along with Sephiroth's behavior after falling several feet into the air isn't out of character, its just exposition.