I am guessing fslconf/fsl.sh but of course it cannot be called that way from /etc. Honestly I would rewrite an independent one. More frankly I would put everything that is really essential in 99fsl and just not put this file at all.
fsl is full of rotten stuff and that's one of them. The only thing that it does that is not reproducible by 99fsl is reading the user ~/.fslconf/fsl.sh file if they have one. And that's very much because the whole thing is not wired in the executable. 
If someone wants to change the default set in 99fsl they just can source a .fslconf/fsl.sh from their own .bashrc (or other .*rc).