I know you are getting many different opinions here. From guys I've talked to, that use -31a's and PEQ-15's, (and EOTech's BTW), going passive and sighting through the EOTech is a "1%" solution, and that is a direct quote. Now granted they were door-kickers and shooting fast at close ranges, but the IR laser was the aiming system of choice.
Now that being said, some guys are going with an additional 1/2" or 5/8" riser, to elevate the EOTech, to allow using it in passive NV mode, for "peer-to-peer" engagements. The extra height allows for the extra length of tube your eye has to sight through, without having to "turkey neck" to see through the reticle. Look down through the threads when you have time. There are several good discussions about this stuff. I run a Halosun 515, on a 1/2" Hahn riser, with a head-mounted -14, set at infinity. The reticle is nice and sharp when sighting through it to the target. I found that I just like the extra height for all-around shooting, with or without NV, not just to have the option of passive NV.
But I would hazard to guess, that using the IR laser is still the most common aiming system in use. At least with guys that have BNVD's and top-end lasers.
Not sure I quite understand what you were asking in the last paragraph, but no, I haven't noticed any problems with muzzle flash, or back pressure from my can either. I get a little carbon blowing out around the gas port, and a lot in the chamber, but nothing that effects the IR laser (or illum), or the RDS. In reference to thin-filmed (or filmless) tubes and recoil, that is usually a -14 in the weapons mounted mode. Regardless of what they're rated for, I don't think it's a good idea, especially when head mounted systems work so much better. So if you are going with head-mounted BNVD's, this is a non-issue. Speaking of films, the new L3 Filmless WP are reportedly pretty good.