I use PMK and Ilford Rapid Fixer or Hypam regularly. No difference in stain (and I have done the side-by-side test). Getting rid of the dyes is a matter of using fresh-enough fixer for long enough (extending fixing times slightly won't hurt film) and washing thoroughly. Don't use a sulfite bath if you use staining developers; it can remove the stain according to Gordon Hutchings. This includes Hypo-Clear and other wash-aids.
Personally, I prefer a slightly acidic to neutral fixer for film. Alkaline fixers can re-acitvate carried-over developer and sometimes cause fogging or streaking if one is not careful about turning on the white light too soon.
I had some batches of TMY that had a dark blue/magenta stain that just would not clear with the normal methods. I solved the problem by giving them a final soak in a weak sodium carbonate solution (metaborate and bicarbonate worked as well). This was a standard part of my processing for some years. Recently, however, the problem seems to have disappeared; no dye stain after the film comes out of the fixer. I changed nothing, so it was something to do with the film itself.
Best,
Doremus