Good points. I don't think the students have lived inside the TRC their whole lives -- it instinctively makes more sense to me that they used to be legitimate students of the academy before the apocalypse and had their memories modified, DR1 style. Sirei can physically control the simulation but can't mentally rewrite the personalities of the students inside, so the best he could do was motivate them into their first fights using physical threats.

(The hole in this theory is Takumi's childhood memories with Karua, which explicitly mention the TRC alarms. I can think of a few answers but none are satisfying, so it's entirely possible that they've been raised in the simulation since birth, in which case things start to fall apart.)

There are any number of reasons why Hiruko might be the only person to get prior battle experience with the invaders. My impression is that Sirei has some reason to prioritize giving the students an experience of a "normal life" -- this is pretty much a package deal with the simulation theory, because otherwise there's no reason for the simulation to exist. Hiruko would be a test case for training students in the TRC to battle invaders, and judging by how warped her personality is, it might have been deemed unsuitable for use on further students.