Spent some time looking into it. No breakthrough yet but I did notice that IRQ 0x02 (which is linked either to VBL, completion of processing on the Real3D, or both) is probably the only IRQ that needs to be fired during the Scud Race intro. IRQs 0x0D could be disabled without any visible impact. Interestingly, when 0x02 is disabled, the game gets stuck waiting for decrementer exceptions. Next, I'll have to disassemble the IRQ handler. I've done this several times over the years but always forget to save my work. This time, maybe I'll just commit my commented disassembly to the repo. Once I understand the IRQ, I'll have to dig in and figure out where the game is triggering the command port writes (0x88000000). I generated a trace of all subroutine calls during the FMV sequence so I should be able to home in on it. The game goes through dozens of subroutine calls per frame (*excluding* those triggered inside of IRQs), which is more than I expected in the FMV sequence!
My hunch is simply that 0x88000000 triggers an "action", either processing the texture FIFO or, if empty, rendering a frame, and then generating an IRQ. I should also check to see if games ever disable viewports when uploading textures mid-game, so that when 0x88000000 is triggered, no frame is rendered. That would be an even simpler protocol.