I determined how to accurately re-time runs, so I figured I'd put an explainer here.

I use Avidemux to re-time runs, as it is a very simple and straightforward program that allows you to set an A and a B point, then determine the elapsed time between them exactly.

For RTA runs in Excitebike 64, the timer starts when the player presses A on the Rounds preview screen, but the game takes a moment to acknowledge this press on-screen. Therefore, simply timing from the first visible change (the right side of the screen begins darkening) to the final frame (the frame the "Press START to Continue" dialog pops up at the end of the last race) is not correct.

I used Bizhawk's N64 emulator with frame advance to determine how long between when the A press occurs and the first darkening frame, and came up with 6 frames, or about 100ms.

Therefore, to accurately re-time a run, measure the time from the first darkening frame on the Rounds preview screen to the "Press START to Continue" text appears, then add 0.100 to the final time.

Reference timing frames:

(The above frame takes place 0.100 seconds after pressing A)

I've just been timing from the frame the wipe transition starts without adding time for the button press; assume that's what others were doing