I've been happily thumping away on bolt-on's for about a decade, and tend to keep my EQ flat. I just bought a neck-thru and discovered that the sound I was getting from my amp is actually pretty boomy and that my bass actually needs a bass-cut to keep the low bass under control. I'm assuming that I have been missing lots of fundamental all along and that the neck-thru actually has a flat response. I've always favored 1x15 boxes, but I'm wondering if that's because they had the screwy EQ a bolt-on needed to sound good? Has anyone else encountered this?
I don't think you can reduce this to bolt-on vs. neck-thru. Another NT might work fine where yours doesn't.
I have two basses with a similar problem. I have a graphic EQ on my amp. I find that I can adjust the graphic EQ when switching from one bass to the other to compensate for the variance in bass response between the two.
JMX is right, it's not how the neck is attached to the body, it's simply a difference in basses. Do the basses you use have active electronics? If they do, which mine do, you can set your amp COMPLETELY flat (no cut or boost), or very little changed, and simply use the active electronics on the bass to do the modifications. This means you can switch basses and not have to fiddle with your amp on stage. Works pretty well!
Check out MTD.com Mike has some discussion on this. Also check ot Fbass.com - George F. also discusses this matter.