So, I take it the HK factory rail sits lower than the HDPS rail? Is that right?
I opened up my front sight, and have the FFII mounted on an HK rail. I like this set up a lot. The front sight does take up some of the sight picture, but that isn't an issue for me. Both eyes open, the front sight kind of disappears anyhow and I can just put the dot where I want it. If the dot goes out, or if I need to snap a shot quickly when it isn't on, I can just drop right down to the irons.
I use this sort of set up on all my guns, and I find it works great for me.
My only concern with the FFII is that it is no where near the quality that I normally go for. I bought it, originally, to test whether I like the micro sight concept. I do, so I bought an RMR. It is a nice little sight.
I also have a Meprolight M21 tritium sight, and I have used other Trijicon's tritium products. The M21 has the brightest reticle of them all - but even it is very prone to wash out. For range work, hunting, or so on it is wonderful. If you're using it with an eye for any sort of home defense or combat application, they are really no good. If someone points a flashlight at you, you lose your reticle. If you have a bright flashlight on the gun and turn it on, you're going to lose your reticle.
Tritium systems are great - but you absolutely need to have cowitness ability if you're going to stake your life on it.
Even then, it doesn't make a lot of sense to me for most applications, to tell you the truth. An Aimpoint on setting 7/10 can run on a battery for 5 years 24/7. After 5 years, your tritium is going to dim fairly significantly. Two batteries will last you longer than the usable life of tritium, and you can actually adjust the reticle brightness as you see fit.
I use my RMR on a handgun. I like it because it has a nice slim profile, draws nicely, is always on, and I have it co-witnessed with my irons. If Aimpoint made a similar profile reflex sight with their life-battery life ACET technology, I'd switch.