the flap is a cover. getting in the way is a matter of usage and preference. its velro closure but can be blocked so its just a flap over vs locked down.
I use the Domke F-5xb and c. Similar footprint, but the c is deeper, so I generally use it with a DSLR, unless I want the NEX and some other stuff (water bottle, etc.).
I like the Retrospective series for DSLR gear, but I prefer the more lightly built Domkes for the NEX stuff.
I use a cotton Domke F-803 satchel knock-off made by Safrotto for my NEX-7. I'm using the body with small Leica rangefinder lenses so the bag comfortably holds the body and four lenses. The eBay seller incorrectly identifies the bag as an 804, it's an F-803...