I’m more concerned that the front quarters and rear quarters match fit, size and tint than whether it is flush it not. The recessed are cheaper apparently than the new flush ones that camper glass are promising. Cheaper is good as I need to pay for a clearcut conversions yo-yo bed and rails system and floor to be installed.Aftermarket ones are usually recessed, so different design. Not seen any reports of problems, but of course don't look as flush!
Have seen mention of VGC flush windows on the forum, and the THQ ones have been promised for some time.