One of the problems was, that FASM simply broke on source files larger than 64k.
I remember that problem, it was because BMax was using an outdated version of FASM that had a bug, and the problem was remedied by upgrading FASM.
That's not technically accurate.
It is a third-party tool that BMax utilizes.
I'd maitain that changing it is very much customising blitzmax,
You are not touching BMax, you are touching a third-party tool. If you don't know the difference in a bug being caused by Bmax itself, or a bug being caused by FASM, you probably shouldn't be using either.