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A "native Linux" label doesn't automatically mean fewer layers or better longevity. Unity's Linux export targets Vulkan/OpenGL and uses SDL2, but the core engine is proprietary.
Something seems to be missing here...
Unity's Windows support targets DirectX (I guess), which by Proton is translated to Vulkan/OpenGL. So yes, for Unity exports, which you seem to be talking about, native Linux does mean fewer layers.

Many of us still equate "native Linux" with fewer dependencies and better long-term stability. In reality, both paths are layered. The difference is who maintains those layers and how quickly fixes propagate when things break.
Who maintains the .exe format or the DirectX Interface? Ah...

We assume native equals independence.
Never heard that. I assume native support means native support.

Unity’s open-source dependencies are compiled and linked together with Unity’s proprietary engine code. Many issues can’t be fixed by the community. You'd need changes inside the closed Unity runtime or the game project itself.
It was possible for the Unity problem I'm actually aware of though, a strange interaction between a 10 year old Unity weakness and Steam using CEF in a certain way 10 years later.
(Good luck btw for getting a bug fixed for a Windows version of a ten years old game...)

https://ein-eike.de/2025/06/05/fix-for-old-unity-games-for-linux-not-starting-anymore/ [External Link]

So here’s the question: For closed-source commercial titles (not community-maintained OSS like 0 A.D.), what concrete benefits does a (proprietary) "native Linux" build deliver that outweigh Proton's faster fixes, wider hardware coverage, and transparent maintenance?
For the vast majority of my Linux native games, I don't need fixes, have never had a problem with hardware coverage and have the most transparent OS-to-OS translation layer possible: none. So, I don't see all the greatness you want to have outweighed in the first place.

What do you get by having a native version: Your system is supported, which seems to mean nothing for you, but much for me. And you are entitled to support by the developers. We lately had a case in the Steam forums again where somebody was told that the devs don't care that their game stopped working with Proton, they only care about Windows.

https://steamcommunity.com/app/221410/discussions/0/601915789280286287/ [External Link]

(Yes, there's bad support for Linux version as well sometimes. And for Windows versions used on Windows.)

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