Any way to complete the optional objective (release/contain the prisoners under the Silver Dream matrix)? I can jack into the Matrix in the first fight, where there's a time limit of 5 rounds before the computer shuts down, but all I can see are the drone control and safe lock modes. I went past the prisoner level all the way to the entrance area, and still no jack-in point.

Didn't see a jack-in point either. There is one in the final room (or at least a computer that looks like it), but it's not accessible. I suspect that is one of the things the latest patch fixed.

I thought I'd maybe missed a portal in the Hot Lab matrix, but nothing. Then I take the tram, and some prisoners attack me, so I guess I should have liberated/contained them before that – after talking to the head scientist and before going back through the prison level. But I can't find the Silver Dream matrix anywhere.

I discovered that myself not long before you posted your solution. I replayed the whole section from the Hot Lab. Apparently I didn't notice the consoles, even though Gaichu had to follow one of the guards there during combat. Maybe it was a bug; I've since updated the game. But for some reason I thought the controls for the test subjects were inside the matrix.