After being curious for a long time exactly how much time VC saves over N64 in any% runs, I finally did a side-by-side comparison. It turns out that VC doesn't save any time at all!

I used my PB on VC and compared it to michaelgoldfish's PB on N64. I removed all gameplay so that only the screen transitions and resets remain. In the end, N64 is about 1 second faster, but VC might save a tiny bit of time on Bowser due to no lag.

VC also doesn't require 2-2 lag reduction, which saves about 2 seconds if you don't use that strat. If your 4-1 uses the method where you enter two huts, then VC will save you an extra second or two because of one additional screen transition. Between Bowser, 2-2, and 4-1, VC might save 3-4 seconds for most players, but the time becomes more negligible as the run becomes more optimized. This means neither console will be a stronger contender than the other for WR, and you're free to use either one and trust that the leaderboards are accurate.

VC benefits much more in other categories because there are more screen transitions.

Edit: Not included in this video are level load times. VC loads each level about 20 frames faster, so that's 2 seconds saved for VC throughout the run. It's still close enough that there isn't a strong difference between the two consoles.