The web version has less performance and some features that you can't do in the web version. Not really much of a change.
Viewing post in Baldi's Basics The Ultra Decompile comments
I found a few actually.
1. In web version, beans spits gum random and not the player but on windows version he will always spit his gum towards you.
2. In web version, you can press enter to always skip playtime's voices but in the windows version you can't press enter when she says her numbers.
3. In the web version, the game is not that good for optimizations, but in the windows version, it runs very smooth.
And that's it.