Those recomendations are because:
A. Ported chokes bleed off gases, potentially interfering with how the wad brakes deploy and can cause poor patterning because the wad requires those gasses to actuate the fins on the wad.
B. Ported chokes of the wad stripping or more to the point WAD COMPRESSING types can strip off wad material causing the same problems as already noted AND can cause a build up of the plastic wad material in the choke and potentially higher and dangerous pressures. Have I ever seen one single truly documented case where the latter happened (other than with the BDS chokes last year that were reportedly due to a bad batch of steel)?...nope but it's not to say it couldn't happen! FWIW, the FC wads actually perform pretty darn well through my Jelly head choke, despite the porting and wad ring...