I have Troy BUIS on my M&P 15, along with an Aimpoint ML2 on a Larue cantilever mount.
The lower third thing is going to depend on the mount more than the red dot. The gun above has the lower third set up, my Armalite M15A4(C), with GG&G BUIS and an Aimpoint M2 mounted on a GG&G cantilever mount give a dot/iron sight centered in the tube arrangement. (As a side here on the different sights, I find the GG&G to be the better sights between the two. The Troys are not as well made, and have a lot of "wiggle" in them, and I dont shoot as well with them as I do with the GG&G's.)
No matter what, if the dot is zeroed the same as the irons, when your head is down on the stock, nose to the charging handle, and youre looking through the irons, the dot will be on, or "halved" by the tip of the front sight.
While I do have BUIS on those rifles, I rarely use them and both guns have them "down". Its much nicer and less distracting to shoot "uncluttered".