So if I were to do a Remastered Sprashfecta am I allowed to do the Spyro 2 permanent supercharge glitch and bring it to Spyro 1 and 3 or is switching between files not allowed?

I believe that is the route yes. Iirc thats how you do 337s so...

https://www.speedrun.com/spyrortconsoletimetrials/run/yj3grw3z

Standard rules apply for multi-runs. Typically if something is allowed in the trifecta, it's allowed in the sprashfecta. Only problem would be if you did the games out of order and wanted to mix in Crash between the Spyro games, which is okay but it means you'd have to set up level storage again.