I don't have a reference right now to the source, but I believe that a well constructed guitar is more important than the type of neck join. For all guitars, the strings are attached to the neck, the neck to the body (ignoring the multitude of broken gibsons lol), and the amount of neck wood is not insignificant, so you can't discount the tonal impact of the neck wood.
Based on this, I would say you'd find the bolt-on maple-necked guitar brighter than the set-on mahogany-necked guitar to some degree. Both should retain that aggressive attack that the aftermath makes its own, but I would expect a bit more in the upper mids and highs from the maple neck instrument.
Just my ill-informed web opinion, wait for some professionals to show up for a proper answer ;)
Roo