You can, however there are a few things to take into consideration. For one thing most text in the game is unskipable meaning you would lose quite a bit of time due to having to textboxes alone. the only advantage the Rare Replay version has as far as I know (and feel free to correct me on this) is that it doesn't have any of the lag that the N64 version has.

I'm new to the TPP Scene, I tested out the whole Chopper skip on the most recent patch and I'm almost certain that Chopper skip was patched. I gave it about fifteen to twenty tries and could not get it to work. If this is the case then like Dekuking said the categories need to be split into current patch and old patch runs.