Yes, that's why you still have these 'ubuntu_12' folders in the Steam installation, since they have never updated this in the past 9 years. So in reality, native Linux development has pretty much failed, and they have put all their money on Proton. That is probably the right decision from a business perspective, but it's pretty much a defeat nonetheless.
What's wrong with it? Having the Windows APIs turn into a portable abstraction layer is certainly amusing, but having wine sitting underneath the program is really nice (essentially for the same reason a VM is). For one thing, winedevs are way better at linux support than random gamedevs.
So, I don't care whether a game is native [1] or run on an emulation layer as long as it works and performs reasonably well and, most importantly, it is supported.
[1] the reality of course is that many, but not all, native ports still run on some sort of buggy, proprietary translation layer.