On the other hand, I don't understand, why 'm68k' is .cpu and not
.arch... strange.
m68k-atari-mint-as --target-help
The key points about the main issue are:
1) Understand how arch/cpu are supposed to work in the binutils
2) Determine if the new GCC 4.7 behavior is a bug or feature
3) Fix the FreeMiNT sources accordingly (4 files)
True. IMO the .cpu only solution should work, but the -m68020-60 => -mcpu=68040 is wrong. Maybe you could rephrase your question in the binutils ML, to be more concrete so it's easier for them to answer (generally speaking, the difference in .cpu and .arch is mentioned in the man/info pages, the fact it's vague is another thing).