1. It doesn't separate program's config, data, and cache; so it is impossible to backup excluding cache, impossible to reset your config without data-loss.
2. It assumes home is infinite, if you are running out of space in home you can't move program files to other partitions. E.G. Flatpack hardcodes its apps data in `~/.var` so if you have a small/almost-full home partition you simply can't install certain Flatpacks.
First and foremost, that I don't get to decide where things go on my own machine, and that if I do regardless, because developers didn't follow a simple standard and instead decided to hardcode things that shouldn't be hardcoded - which is just about the first thing every dev is taught not to do - things will break.
You may not find it important but is it an issue or not?
2. It assumes home is infinite, if you are running out of space in home you can't move program files to other partitions. E.G. Flatpack hardcodes its apps data in `~/.var` so if you have a small/almost-full home partition you simply can't install certain Flatpacks.