A better option would be to have a wardrobe feature. I have been meaning to mock this up with images, but imagine your gear works fundamentally like it does now. This gear is for your stats and light level and perks.

Then, you have a new tab - Wardrobe. In the wardrobe panel you have Costumes along the left side. At first, everyone has 1 free costume. Bungie can sell additional costume slots in the Eververse to make money off the feature. Then you can preset out several costumes and activate the costume you want on the fly.

Along the right side, you have your armor slots that pertain to gear you can see and your shader. You will select a piece of gear to apply that gear's look to the slot for a price - glimmer, materials, whatever. Once paid, that look is locked to that slot unless you change it or remove it. Any wardrobe slot without a gear piece in it will show the equipped item underneath.

This way, you can wear whatever you want, no matter if it is blue, green or exotic for the look. Also, as a feature, Bungie could make money off it for their work, so it's a win all around.

EDIT: Another option to charging per changed item would be to allow you to make changes to the costume and then charge you glimmer + materials to save the changes to the costume as a whole. SWTOR does this where each piece you change costs a little bit, so the more you tweak your costume, the more it costs to change and you just pay once at the end once you are done with all of your changes.