a atmo bov on a AFM will normaly cause you to run rich on gear shift. sometimes people may see a puff of black smoke after gear change on a atmo afm turbo engine. excessive richness can wash the bores which in turn can wear the rings down faster.
i run a atmo bov on my AFM 4agte, the engine still runs fine so it doesnt bother me. though the noise starts to get annoying after a while.
will be converting mine to a plumb back once i make the adaptor.
I have an Atmo BOV on my 3SGTE equipped with AFM (came with the car, when i can afford it im going plumb back too) and most of the time it behaves normally, but occasionally the richness can cause a small backfire after changing gears if the cat/exhaust is hot enough.
To answer your question about how the AFM behaves. My S-AFC shows my AFM opening as a precentage. I have watched this when I change gears under boost, and when the throttle closes and the BOV operates the AFM spikes along with the psssht (sorry, didnt mean to go all technical there ) Because air is now allowed to flow thru the BOV, not the throttle this adds to the richness, and out of whack A/F ratios.
However once the BOV closes and your driving away there doesnt seem to be any after effects to this A/F ratio change. Although some people have posted that their engine runs rough for a period after the BOV operates.