Hi Paul, I can see what you have.
I used to play with a sound similar to yours, quite high gain, very smooth. In my first guitarist life (I used to play in a band in my early 20s, then didn't play for 10 years and started again 2 years ago) I never used the neck except sometimes for cleans or for Santana-like soloing.
Nowadays I use less gain and aim for a less compressed sound, which is sometimes harder to play and keep sustain, but in return gives you punch and definition. It's then where a neck Pickup like the RY makes sense and offers exactly the kind of quality that suits and rounds off this open and rough tone.
Why not try to optimise the amp settings for the neck (i.e. try less gain, less bass, less effects, until a rhythm riff sounds good on the neck) and then switch to the bridge, see if it's an acceptable sound - it's probably very different to what you feel comfortable with now. Maybe this can help understand where in your amp the EQ dislikes the neck pickup and make it easier to find a good compromise for both, bridge and neck.