Okay, here are two ways it can be done (with more detail).
First, no rules. For GameCube players, it's as simple as submitting the time as shown on the stage select screen.
For Dreamcast players, 100 minutes can be re-added for the submission if they were removed for that screen.
And it is provable still, with a video showing the end of the stage and the stage select screen.
If the timer is maxed at just under 100 minutes during the battle, and then the time shown
on the stage select is, say, 14 minutes, it's obvious that this 14 is over 100, and so, must be 114.
Simple enough, right? There was no confusion or arguing over this in the first place.
The other way is to have a "3 times per life" rule. This makes time-freezing useful only if used properly,
since there are limited checkpoints, and only 3 seconds can be gotten from each switch on each life.
Not much trouble there. I still think no rules might be better, but this is the best rule I can think of if there must be one.
EDIT: 300th post. Also, I'm changing the subject.