The market share is never a precise number because not everybody is asked to do the hardware survey, and not everybody who is asked does. But the Linux userbase is small enough that "~3%" is in the ballpark.

Version control of dependencies is not as difficult as it seems. Unix systems can easily implement bundled dependencies like Windows does, even without sandboxed or monolithic packaging formats. The important thing is to tell the dynamic linker (ld.so in Linux's case) where to look for the library files, similar to how PATH is used to locate executables. This is similar to how containerization works to a lesser extent, and the Steam client actually does this by loading its own .so files from ~/.local/share/Steam/.... I'm sure there are additional challenges, my knowledge is superficial and approximate at best.

But the point still stands: in most cases, Linux-native ports are simply not worth the effort, either because of limited resources in small teams, or because of profits in large studios. BG3 and Factorio are definite outliers.