The Wine and Proton devs claim that all of the code has been reverse engineered and written from scratch to simply be compatible with the Windows APIs. Unless that claim is false, or Microsoft has a patent over any systems they are recreating (which is unlikely), there’s nothing Microsoft can do legally. If they did have a patent, getting around it probably wouldn’t be too hard.
Self host as much as you can. Use smaller services when you can’t. And pay for things you don’t host yourself. If it’s free to you, it’s because you’re the product.