The m68k ISA is the same because it was an architecture with relatively short lifespan. Or one can easily say Coldfire is the same arch and that m68k hence struggle with same issues. The many incarnations of ARM is a result of evolution and what keeps it relevant. In context of Linux, this variation is not much of a problem, it is something we are used to, something we deal with all the time regardless of architecture. There is no "win32" for Linux, we use sources.
And yeah, I know what goes on with Linux on m68k, been on that boat since 1994. I believe my Minimig has a uCLinux disk image that I built some years ago. Those people you speak of, they all left because of limitations in Amiga OS, both technically and legally. Amiga OS can never replace uCLinux either, sadly.