Having only built bolt-ons, but owned a few set necks, I get the impression that there are too many variables at play to nail down a particular characteristic of neck contruction against a specific tonal behaviour of an instrument. There may be tonal and/or sustain differences between a set neck and bolt-on, but I'm yet to be convinced otherwise that those differences are far outweighed by pickup choice, scale length, string gauge, body mass, bridge construction etc. I've personally never owned two guitars so similar, with the exception of neck attachment method, that I could formulate an opinion about the matter. The minimal heel on a set neck is attractive, as is the separability/adjustability of a bolt-on. There are ways to minimise the heel area of a bolt-on to alleviate the big block of wood that gets in the way on a Strat (Ibanez's All Access Neck Joint or ESPs tapered neck joint for example). Likewise, there are set neck guitars where the joint is such an unwieldy shape it makes you wonder why they bothered (the heel on a PRS Custom 22 is just plain weird). The first 'proper' guitar I owned was a Yamaha Pacifica, which had an ingenious bolt-on system which just about eleminated the heel completely. The neck heel attached to an aluminium tongue, which fitted into a matching socket in the body underneath the neck pickup.