I assume you are speaking of a cross-compiler.
True but it applies to any installation.
3) There is an additional oddity. GCC requires that /usr/bin/m68k-atari-mint-as should be also available as /usr/m68k-atari-mint/bin/as as well
Yes, you're right, gcc wont compile anything without those symlinks because it invokes 'as' and of course, the first (and only) 'as' found is that in /usr/bin. Can you imagine any reason why m68k-atari-mint-gcc can't search for m68k-atari-mint-as, esp. when it's found during ./configure phase under this name?
And finally, target executables (by opposition to target libraries) should not be installed on a host cross-environment, it is a nonsense since they can't be run on the host.
Not entirely true, because:
1. ./configure isn't aware of (in)compatibilities between build / host / target environments and honestly, what should do instead? Ignore make install for those executables? What if packager invokes it with make install DESTDIR=... command for later (native) packaging?
2. Some executables are mandatory to be there. Perfect example is sdl-config for m68k-atari-mint target. It's invoked from many configure scripts under the name 'sdl-config', i.e. not m68k-atari-mint-sdl-config (there's no such convention, sadly) and guess what? It works well because it's shell script but it returns atari-specific flags.
I just wanted to verify gcc is that strange one and it's really uncommon to place cross compiled binaries in <prefix>/bin directory -- so thanks for your opinion!