There might be a few unforseen problems with certain platforms. I'll admit I didn't test out WebGL builds, but I have heard before that there are certain shader features that straight up don't work on that platform. The noperspective keyword, which drives the affine texture mapping effect, might be one of them. I'll have to test out the CRT effect with WebGL but I really hope it's feasible to get running, but thanks for letting me know about these problems.
That's actually a bit weird that the base texture isn't preserved - if you mean you're going from Lit to Retro Lit, they both use _BaseMap as the shader reference and I think Unity is meant to keep textures in that case. I'll see if I can get that fixed.
With the surface options menu bit, I can probably find a way to auto-open that, although I'm not sure which people would generally prefer. Interestingly, I had to create that whole bit from scratch - I really wish there were a way to just click a button somewhere and Unity just adds that whole section, but nope, it involves a fair bit of editor scripting!