This is just more of me expressing some thoughts that some people might have feedback on.
I used a Kinesis Advantage for over a decade and it made me feel at one with the computer until one day I started to get right hand pain.
I gave it a break for a few years, then got a new Advantage 360 and a Glove80 to see what would work for me. Neither do, both make my right hand feel more cramped than it should. But I'm pretty happy on something like a Sofle or a Kyria, or even a basic TKL - tho still get pain after a time.
I do have cubital tunnel like symptoms but was recently tested and don't have any real nerve damage that can be fixed, so based on the advice of my neural muscular doctor and physiotherapist, I'm still in the prevention stage.
Does the keywell cause the use of different muscles and finger joints to press keys? On a flat keyboard, key strokes seem to move the whole finger from the knuckle. If a keywell results in a curling or stretching motion of the fingers to actuate the keys, that would use different muscles and move different joints.
Another thing would be whether you're using wrist rests differently.