Because Ben had the omnitrix in DNA Lock mode, (not official name, don't quote me) he probably transformed into a naked incursion because the omnitrix wanted to make a perfect transformation. So, he put on the clothes.
No, the new Omnitrix has a modified clothing system, so maybe, since the Incursions have that type of clothing all the time, the Omnitrix gave Ben that clothing. The other possibillity is that when Azmuth was unlocking Bullfrag, he ordered the Omnitrix to give Ben that clothing.
But the modified clothing system adapts Ben clothing by rearranging it. Since we've never seen the omnitrix change the color of Ben's clothes, it probably can't. So why would it form a incursion uniform?
Technically, We all know the Omnitrix symbol dosen't move some where else on the alien unless its a diffrent Omnitrix, So the i pick No, Azmuth probally did something to the Omnitrix to make Ben wear Incursion Clothes, That is why Ben has the Omnitrix Symbol HIDDEN by the Clothes!!
P.S. I think the Incursions would Kill Ben if if they see Bullfrag's Green Eyes so Thats why he wears Shades, But i think that the Omnitrix would never give Ben Shades ( Normally, Just Goggles ). So, Ben just got Glasses and but it on