Different intake restrictions mean the turbo has to spool to a different speed to get to the same mass air flow situation as before, this means a difference in exhaust gas flow as well, which could lead to a change in the engines timing requirements.

Perfectly reasonable to say therefore its good practice to remap it, so im not sure what your issue is?

That said, the effect is likely to be minimal and in most cases with an AFM there will be enough room to manouvre to get away with it IME, but as everyone says, it would be silly to not at least check it over!