it's only my feeling gcc/binutils binaries are wrongly placed in /usr/m68k-atari-mint/bin (or any other prefix, does not matter). I've noticed this when I installed some libraries which produce executable files and if I configure them with install prefix /usr/m68k-atari-mint, they are placed in /usr/m68k-atari-mint/bin what is OK. But this means in this directory are located Atari native binaries and not 'as', 'ld' etc binaries which are compiled for i386 but by some 'coincidence' produce/use m68k-atari-mint code.
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MiKRO / Mystic Bytes
http://mikro.atari.org