The biggest difference between aftermarket housings and stock OEM housings is the projector assembly itself.
Stock housings have bixenon projector housings that are properly designed for HID bulbs. They have the correct parabolic focusing mirror in the projector assembly and the correct cutoff shield to produce an even toned light with minimal glare and diffusion fron the housing.
Aftermarket solutions usually have cheap, halogen projectors that do not have proper cutoff, do not have proper focusing mirrors for HIDs. They are meant for a halogen light to be installed in them. This being said, they do not focus light properly, you get uneven hotspots of light on the ground, and you get tons of diffusion and glare, essentially blinding everybody and you are no better than someone who puts HIDs in the stock halogen reflector housings.
The only way to get proper HID on this car is to buy the OEM HID headlights, or retrofit HID compliant projectors into your car. You COULD make the job easier by buying aftermarket headlight housings, then retroftting a nice projector in those. Imagine a stanley s2000 projector inside an aftermarket headlight housing... you'd have way better headlights than a stock GTI.
The bosch projectors used in the stock GTI headlights is not a very good projector anyways.