You can have Snap, Flatpaks and native packaging running side by side so... and Ubuntu has a unified interface for all of them (the "Software" application). So yeah, another non-problem for the end user.
The end user doesn't have to know what X11 and Wayland are. You don't need to know this to use most software. Just use what your distro provides.
Most of the complexity you mention is hidden from the end user.