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.