I feel you on the thin but flubby neck pickup. I almost always need just a bit of bridge from whatever I'm playing to bring back that BUMP and POW. I find that somewhere between 200Hz-500Hz is where I end up needing that hump eq wise. Sometimes bumping those frequencies combined with whatever lows are being accentuated can get a little muddy. By itself it sounds fantastic, but with a band it becomes blobby and undefined. Felt, but not articulatorily heard. That's when the HPF comes in handy.
Much like when mixing live music and records for bands, I've learned that what I like my bass to sound like by itself does not translate to playing with a band. With a band I need a more "honky" "middy" not as full bodied tone than when I'm by myself. Don't get me wrong, it's still a bass, just with different accentuation points. By itself gimme a Sadowsky pre and watch me roll that 40Hz shelve up and love the bass. Then a bit of top. And a big Smiley EQ will be formed. Then the band comes in and I sound like BOOM BOOM DOOM BOO DOO and it's all blegh. Especially in big rooms where the low waves have so much more space to develop I'll find my self cutting low and boosting mids in such a way that sounds unpleasant solo, but somehow just fits sonically with a group.
I get it man, it's a tough cookie sometimes.