Proton updates can sometimes unintentionally break or introduce bugs and glitches for certain games in which case you can force the use of an older version of proton where the game works best.

Most of the time though the latest version works fine. GE refers to a custom version of proton with community patches applied to faster than official proton releases.

I have used my Steam Deck for roughly two weeks now so I might be wrong but personally the latest Proton version running games through Steam works perfectly fine.