If you look past the package managers, there is less difference than you might think. The kernels and libraries and xdg are largely from a common base. The biggest problem I run into is with graphics drivers for proprietary cards. And that's not a simple problem. It's one reason why one of the major software packages we have to run no longer runs on Linux (windows and solaris only now). Which is a pity.
I don't know why you assert that CentOS isn't a desktop OS though - it works perfectly well as one. Indeed my desktop is. But that's a topic for a different board.
Yes the kernel is largely the same, but not the thousands of various libraries. Every now and then I have to deploy on system A some application developed on system B with diffferent library versions that ends up not working because for some bizarre reason open source developers are very fond of changing APIs every other day. Ugh.
And yes the display drivers, of course. Which card does the user have? Does he use the OEM driver, assuming there is one at all, or the open source driver that of course has different performance and feature support?
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