The big difference that many seem to miss is that a flying suit is an official uniform. (No 14?), whereas I do not believe that engineering overalls are.
The subject is a pretty boring perennial for the haters but iRaven hit the reasons on the head and, as Len said, while most of the army pitch up to work in MTP (or variants of) there really is no rational argument against aircrew wearing flying suits, whether they actually get airborne that day or not.
Personally I think it is a good reminder to those around the stations that think the RAF is about admin rather than Air Power.