Tl;dr it’s likely that some of your hardware isn’t well supported in Linux or have vendors downright hostile to open source (fuck you, Broadcom and Nvidia) and causes you weird issues that almost always get fixed by the community but may not always work “out of the box”
I’ve been in Linux since 2008 and have asked this question in many ways over the years. To get a real answer I’d dig more into the errors you’re encountering. I think that a lot of the “simple fixes” you mention are simply options that some hardware configurations need and some don’t.
Flatpak and Linux in general deal with the same huge task as Windows, which is “support any hardware configuration with one universal solution”. While Windows is given every advantages by cooperative hardware vendors releasing official drivers, Linux is mostly supported by open source reverse engineered drivers.
This means that no “universal” system is likely to work all the time in every case, but that’s ok because it’s all open source and the community finds a way.
You mentioned themes and some graphical packages, do you have an Nvidia GPU? I never had anything but trouble on Linux with them.