I've had my R1 for over 5 years. It has always hit low at 10-15 yards. My sight picture is the front sight dot on the center of the bull. I ordered a LPI adjustable sight and installed it. That cured the problem. I got it sighted in at 10 yards.
Your new sight reminds of a Millett (sp?) sight I had installed on a Browning Hi Power back it the 80s. At the time, it seemed to be the thing to do and worked out well. Now years later, I wished I hadn't done it. But oh well.
I had an R1 in the commander size that shot right to point of aim with 230 gr. FMJ. Never had a complaint with that pistol. My son now has it.