Never had an bolt-on LP, but I'm on Warmoth forum too and there is two major feelings about it there:
1) It change the tone. will give you a more '70s tone...
2) Don't change the tone...
If you get a fatback or '59 roundback I think the difference will be smaller, but if you get a very thin Wizard neck, will be a difference...
Just to add, that difference in tone is no disadvantage, just difference...
For that advantage side I think a bolt on neck is more advantage because you can just change it if you brake the headstock or anything else...
That is the only think I count in that side (that I remember now :roll:)
EDIT: From Warmoth I would have a bolt-on LP, but for custom would be set-thru or neck-thru...