Having played this game hundreds (if not thousands) of times, I can assure you that it does make a difference. It's like saying "memorizing a map won't help you navigate the streets because the map looks nothing like the streets".

I recommend you give it a shot and see if it helps you. There's also a couple settings to "invert" the fretboard to your preferences if that's what you prefer.

Lastly, it's really fun to actually play the game with a real guitar. If you click/tap the note on top, it requests mic permissions and you're all set to now play with a real fretboard.

P.S. If you go down the real guitar route, try the Arcade Mode on find the Notes. It's the most fun thing I've ever built...a space invaders style game on the fretboard. But driven with a real guitar.