We’ve got a somewhat similar system Joey, I’ve a Luxman 507UX integrated, a VPI Classic 2 turntable with an Ortofon 2M Black cartidge, and Magico A3’ speakers which are quite revealing.
After reading your post, I’m listening right now to some earlier Warner/Reprise Neil Young albums purchased when first released. "Cowgirl in the Sand" off Everyone Knows this is Nowhere and "Cortez the Killer" off Zuma are first up. "Cowgirl" is harsh in the upper frequencies so I can see what you’re saying there. The lower frequencies are not lacking. I played with the treble control as Erik suggested and that seemed to lessen, but not fully correct, the harshness. "Cortez the Killer" was fine, kind of an average recording, but not unlistenable at all.
I’ve lots of Joni Mitchell vinyl records and none of them seem flat sounding or lacking in any way except for one odd German pressing, I can’t recall which. On the contrary, most of her recordings, both vinyl and
CD, seem to be especially well done.
Now there are some real dogs out there that fit your description, like the original Layla and the Stones’ Let It Bleed pressings, which need to be replaced if you love them as any right thinking person should. But the Neil Young’s are definitely not nearly as bad as those two tragically truly un-listenable albums . Maybe your Luxman 509 is that much better at helping reveal things the 507UX masks. It would be interesting if you could borrow CD versions of your Neil Young’s and see if you hear much difference in how they sound. Or take your Neil Young records to a friends to hear them on another system.
Mike