I work in software now, but I have an electrical engineering degree and started my career on a project developing a radio. Our project probably had ten or more electrical engineers on it, and only one or two of them really understood the RF side of it. It's a very specialized skill -- even EEs with >20 years of experience would describe things as black magic.
So I don't think you're alone feeling this way. Even with a good foundation in the theory and math, I think most people hit a wall with radios at some point. All the people I worked with who intuitively "got" RF stuff had been doing nothing else professionally for over a decade.
A long time ago, worked on a comm satellite program. It used a whack of tuned cans to combine high powered transmit signals with harmonics in each others' frequency bands to feed into the antenna. I once asked how they worked. The answer was 'magic'. I mean, they were physical RF filters, but no one could explain or reproduce how they worked. There was this one guy who could tighten the screws that adjusted the inside baffles so they 'worked'. No one else could.