The initscript for xfs will overwrite user edits to fonts.{dir,scale}. This seems to be rather antisocial behaviour. I have quite a few TrueType fonts installed (in fact I use no bitmap fonts if I can help it). For some of the fonts ttmfdir output is not exactly as I want - for example it gives "Swis721 Md BT" as the name of a Bitstream sourced Swiss721 (aka Helvetica) font - the Md is really the weight (medium) so (IMO) souldn't be part of the familly name - to be fair to ttmfdir I think that this is the name actually recorded in the font. Consequently I have a hand-tuned fonts.dir for these fonts, unfortunately it gets overwritten every time I add a font to the directory (which is rather annoying).
This seems to be the intended behaviour of the ttmkfdir program. I do not see it as a problem. The author of the program will have to change the behaviour if it is to be changed at all.