Disagree strongly Tymeaus,
It takes a large modification (4 mod slots) to turn most weapons into BF or FA... there's only a small handfull of pistols which qualify for this upgrabe by having BF already built in (making it a small modification of only 1 slot). All of which have the problem of low ammo capacity (and ammo increasing mods do increase weapon size btw).
If you are using up mod slots to do this, again, there's an oppurtunity cost in that those mod slots could have gone to other purposes improving an actual machine pistol. You can do an awful lot to a weapon with 4 mod slots.
Also speaking from firsthand experience... I've seen a .45 pistol go full auto. Cosmetically you wouldn't have noticed any difference (unless you looked at the worn sear plate causing the weapon malfunction). So the mod rules strike me as quite good on this front in which mods make things harder to hide and which ones don't.