thoughts on this subject are all over the place and vary quite vastly. i'll give you my take on direct mounting, and why it doesn't effect the tone. pickups are electromagnetic in nature, they pick up variations in the magnetic field. wood is not metal, it does not effect a magnetic field, so i feel mounting directly does not effect the tone, because there is no added variation in the magnetic field. things that effect tone significantly are things like what kind of frets are used, what kind of strings are used, anything that could percievably effect the magnetic field. wood is organic, its not going to do that. but my theory also opens up another can of worms, which i also have a theory on, which is, why do different body woods effect tone? and i think the answer to that is all in the strings. different woods will accentuate different frequency resonation in the strings, so the wood actually effects the way the string vibrates, which is what is picked up by the guitars pickups... again, its all theory, and just my thoughts on this, other people swear that direct mounting pickups has a tonal effect, and they are certainly entitled to their opinion.
by the way, make templates, and use template bits to route your cavities, then you don't have to worry about if your cavities were neat enough for it, cause they'd be just like your template.