> You'd hope libc wouldn't break.
glibc is quite good about ABI compatibility - not any worse than Win32.
X11 also has a stable protocol. Even with Wayland there is Xwayland for backwards compatibility.
OpenGL and Vulkan have stable ABIs.
Your program location doesn't matter - unless you are installed via the package manager (in which case the package specifies the location) you can load everything relative to the binary.
User config location is gained a new standard for where you should put things to not mess up the home directory but that does not break anything. Old programs can still write to ~/.yourfancydotfile.
Evenvironment variables only matter if you wrote your program for them to matter.
Preinstalled libraries are irrelevant - ship your own like you have to do on windows for anything that is not part of the base system.
Acceptable keyboars shortcuts and standard dialogs are integration concerns and not strictly needed. Not saying that you shouldn't provide DE-integration where that makes sense but that can be done on top of sane fallbacks. Also, there is now a cross-DE API for standard file dialogs: xdg-desktop-portals
.desktop files have been standardized for a long time so you should not have problems registering file types - it is of course up to the DE to manage the default and that is a good thing.