My take on it has always been that special weapon still leave the standard weapon (e.g. bolter) in place and are just an additional weapon. If that isn't the case then it could get messy and I'll have to look at it again, but I always worked that way because it was simple maths (unit size * trooper cost + extra equipment cost)
Forgot to mention this. In this case at least the special weapon replaces the bolter. How important, in the grand scheme of things is debatable, after all one would hope the player knows their army.
Another practical example is found in the Terminator squad. For every 5 models one model can replace the stormbolter with an assault cannon or heavy flamer, alternatively buy a cyclone launcher in addition to the stormbolter.
Brings up another "interesting" problem. (Because I remembered it)
Assault Terminators have a pair of lightning claws, but any can swap them out for thunderhammers and storm shields. That's 2 separate items. That ideally would modify the stat line. The hammer increasing strength and the shield giving a better invulnerable save.