As mrgmhale posted, it came down to the limitations of the AC compressors. Ford was utilizing York and Tecumseh AC compressors which were as good as any in the 60s and 70s. The Tecumseh had a cast iron housing and was production installed in many F600-F800 trucks, yet I still have seen them come into the shop with a large "Ventilation" hole in the side of the compressor.
The main problem with the 3.91, 4.11, and 4.30 cars was the load imposed on the compressors when the sudden increase of extreme RPM's subjected them to stress they just were not engineered to handle. I believe the 3.50 AC restriction was a little warranty wiggle room for Ford and the inevitable warranty claims they knew would be coming if they didn't draw a line in the sand. In the 60s and 70s, you could not get AC with any solid lifter engine since Ford knew how they were geared and how they would be driven. This restriction would have included all 271-289s (High perf 289), '66 428 Police Interceptor, 427's, and all Boss engines.
You could do as I did in my Mach 1 and just cut the AC off if you thought you were going to get involved in some sort of red light "Confrontation" or any high RPM cruising. My '85 GT has a micro switch at the carburetor, so when you go to WOT, it opens the circuit to the field coil. Nice to have, but also just as easy to turn the AC off.
I switched Money Pit #1 ('71 M code with AC) from a 3.00 to 3.50 ratio, and the smile factor outweighs any extra cruising RPM or milage drop!