The whole reason for a BOV is to bleed off excess boost pressure in the manifold when the the throttle plate closes suddenly. The reason this is bad is because the denser air can hit the throttle plate and be reflected back toward the compressor wheel in the form of sound energy, which attempts to stop the turbine shaft suddenly. This is a lot of undo pressure on the turbo, and this effect running through an intercooler can actually use the intercooler as a reverb chamber that may or may not amplify this sound energy depending on design.

The bottom line is that typically if you're running a FMIC, you're normally running more PSI than the wastegate can cope with in event of a sudden close of the throttle plate. This of course can have other undesired effects such as boost spiking, additional turbine stress, etc.