I built a similar setup a couple years ago. I used the B-square saddle, but I'm sure it's similar. The truglo gobbler stopper on the saddle does sit high, but the raised comb of the shurshot stock makes it fit well (in fact, shooting a bead with that stock would be just about impossible)
My suggestion is to give it some time, try it at the range. Keep in mind you've built a shotgun that is now an aimed fire gun. Traditional shotgun fit for wing shooting doesn't necessarily apply. The saddle mount and truglo dot is the cheapest / easiest option - but I've had no complaints.
If you want lower, more streamlined- you'll have to do what you said regarding drill & tap with low profile reflex.