One chapter of the story has a giant sized character getting rid of extra mass by magically turning it into light in one of those “barest nod”situations.  I posted the story to the intarwebz and not long after that, someone proceeded to berate me for my misuse of matter/energy conversion.

All I could think was, “Wait, with all the stupid crap that goes on in this story, this is what you decide to get upset about?”

MORAL:  If you’re going to handwave, handwave big.

I’d say you got it on both counts. One thing we’re seeing here is the distinction between Dave’s identity (his nature, as you put it) and his  body. The transmogrifier would have to be about three orders of magnitude more advanced to change the former.

Note that the transmogrification is incomplete, even superficial.  As indicated previously, the cigarettes are essential to Dave’s nature, and he retains them (and the odor) even in Madblood’s shape.

Helen still recalls Madblood’s blush from their last intentionally romantic encounter, such that she can directly compare to Dave.

Unless you do, obviously.

Obviously Helen’s discovered one of the principles incorporated into what’s called “holographic cloning” in the fifty-first century, by which a microscopic image of oneself, including all memories and other acquired characteristics to date such as wardrobe, can be injected into oneself to hunt down the virus that’s taking over one’s body, ennabling one to save the day and then keep the robot dog.