It appears you can rename (or remove) the specs file so it no longer gets used, and simply add the -mafrlcsj option to the project Global options/Additional options. They appear to no longer try to 'block' the use of -mafrlcsj when they move you from the bin executable to the bin/bin executable like they did previously (before adding in arm compiler). The specs file was a way to bypass the removal of the option by adding the option after they were done looking for it. A specs file could probably still be used instead of adding the option to each project, but not sure how at the moment as it appears the mips side is happy with the cc1 addition but the arm side is not (and the specs file could be moved to a more compiler specific folder so the mips version could be different than the arm version).
I hardly touch the pic32mm anymore, and for the samd10 I have I added the arm gcc compiler (downloaded from arm) as another toolchain option, but then requires some extra work to get it to work (replacing xc.h to the mcu specific include, or something). I would tend to want the arm supplied version of the gcc compiler as its a newer version and is used by everyone else, but I'm sure there can be good reasons to stick to the xc32 version.