I had this issue too, then I realized, WebGL build actually might be using the Mobile pipeline settings files when it exports, so any shaders you may have had for it aren't being added! (especially if its post-processing render features etc)
For mobile export I conditionally changed which render data file was being used, and added specific mobile and desktop render features to be used. Hope it helps.
Edit: However, I used unity, so maybe GoDot is totally different, my bad.
Viewing post in Midnight Joker jam comments
Thank you for the tips. The render pipeline itself is fine I think. It has to do with some features I used which doesn't support very well in webgl. And honestly, now I don't really want to spend so much time fixing it. In the end, these web optimisation skills are of no use, right? since most of us will be publishing our actual game on steam, and not on web.