This may be great or terrible, I'll let others chime in.

I always understood theory as the fretboard being a matrix of "a.bc.d.ef.g." where the "." is disallowed by that key. If you learn modes and chords as shapes, you realize every key is just that matrix moved around a bit.

Where it messed me up is I don't think in numbered chords, I think of what the "c chord" looks like given the ionion is now centered on E string fifth fret.

The advantage is you'll know very naturally where all your major and minor thirds are, as well as weird stuff like diminished. If you ever do jazz, it'll be easier for you to flat something or add a 13th.

What I'd suggest to nail the "feel" of different chord progressions is just laying some runs over the progression. You'll figure out pretty quickly what number they're treating it as because if you're playing ionian when it should be mixolydian, the notes will be off. That implies your matrix is in the wrong spot and needs to be shifted.