I think that, while, yes, fragmentation hinders a system, it is also its saving grace, as it also stops a given family of systems from growing into what made the competition problematic.

Taking the Program Files folders as example, they have limited read/write permissions on Windows, so whenever possible, I try to install them onto a folder I make in the root of C:. But more and more, since at the very least Windows XP from what I could observe, Microsoft is training users into using only the users folder, and less and less programs give an option to install elsewhere, installing only on the Program Files folder instead. Meanwhile, on Linux Mint (my distro of choice), if AppImage (my to go medium of programs) isn’t working well, I can always fallback to other means, such APT directly or downloading its .deb files then extracting them, getting from flatpak, compiling it myself, building a custom AppImage, running on a VM or emulator, or in the worst possibility, I make a dual boot between Mint and some other distro.

Also, although there are many package managers, from my experience, they usually work similarly. Some changes in syntax, options and names, but nothing outlandish. It would be, I think, like someone learning a close language to his/her mother tongue. And from experience, you can even organize installations in a more standardized way, although it will take some effort from your part to figure out how, since some adaptations may be needed (java 8 and sdl ptsd intensify).

And lastly, from what I can observe, stuff in Linux more often than not share logic or even methods with a lot other stuff in the system. Dunno if it’s a bit of a bias of someone that’s using Linux for a few years already, but the fragmentation usually feels superficial to me, with distros being more tweaks of the ones they stem from, and major changes being better observable when distros are sufficiently far apart.