I had the exact same problem with my magnifier angled up a bit too high, I actually have an identical set up as you. A simple fix, that metal riser piece that sits in the front, take that out and it will solve your problem. I put a very thin piece of rubber (or you can use electrical tape or the soft side of velcro) to act as a bit of a shim so it sits nicely. Just make sure you tighten the QD mount to the flip to side mount so that way it sits nice and secure. If you're not sure what I'm talking about let me know and I'll post up some pictures of what I did when I get home tonight.
Another thing to note as well is I wouldn't recommend zeroing it with the magnifier up, with mine it has a bit of play to the left and right so I would have to sometimes just tweak it a bit so the red dot visually looks centred. Then again, I'm not intending to use my magnifier to take precise shots, its more or less to track and ID targets at a bit of a longer range. A rail mounted spotting scope more or less...
Hope that helps!