I suppose it depends on how much wood Warmoth allow for their heel.
You may be ok depth wise (i.e. carving and sanding the joint similar to an AANJ)
The problem you may have is the length (the length that the neck inserts into the body).
Fender type joints are routed to a standard length, if there was enough space in this (I've never compared them with AANJ, although having just looked at a body in the corner you may have enough to fashion a very close AANJ style) you could lop off the right side of the joint (looking from the front) with a coping saw and contour it with sanding to follow the AANJ profile.
I assume Warmoth don't pre-drill their neck fixing holes so there is no problem there, and having another thought, Fender style joints do tend to be quite bulky so their should be enough give to shape it.
Your main worry is how deep the neck sits in the
neck joint.
If it sits too low and the fretboard ends up beneath the rout in the body you'll have to make up the space and fill with a veneer or something and if too high (doubtfull) then some carving out of the pocket will have to be done.
I think their is some sort of standard though and most
neck pockets seem to be routed around the 20mm depth.
Just to add, if that Neck you have lying around is a 24 fretter then you're probably bang out of luck, unless there is enough space between the end of the fretboard and the first pup and you can put the bridge in the right place to make up the 25.5 scale length.
If pre-drilled for string through body then it's a no-no.
Steve