Source ports to Linux are actually pretty rare. Most big games with a 'native' Linux version are non-native in exactly the same way as Proton ports— they run using a custom compatibility layer based on WINE or something similar. Often the port is of such high quality that you wouldn't be able to tell (Feral Interactive has done a ton of great ports this way), but this is still how most are done, especially for AAA games.
(In that sense, developers (or Linux porting studios) switching from their in-house compatibility layers to Proton isn't really a change in terms of those ports being 'truly native' or whatever.)
I wonder if what we're starting to see, rather than the inferiority of source ports, is actually that some of these alternative compatibility layers are just no longer keeping up with Proton, since Proton/WINE has such wide use/testing and rapid development these days.