It makes sense, but you're wrong.
The neck, as it stands, does not have a fingerboard, but one will be added. This will have a thickness (likely) of 1/4". Since the neck is straight (ie. no angle), it won't be able to work with a plain mounted TOM. The TOM will have to be recessed in order to get any sort of playable action whatsoever.
Just like how... Godin... does it.
The alternative is to make the fingerboard very proud of the body, which isn't completely unknown; however, that would require either a fingerboard of bizarre thickness or some sort of extra material between the laminated neck and the fingerboard, which strikes me as not something one would want to do. Plus, as you've pointed out, it'd require making the back of the neck far too thin unless a baseball bat grip is what he's after.
So yes, recessing the TOM is the preferred option in the absence of a neck angle.
Alternatively, if the parts haven't been ordered yet, he could just get a hardtail strat bridge instead of a TOM.
Greg