Well, I have purchased a Fender Duo Sonic body (I.e the same as a Mustang or Music Master) and was intending to put a reverse headstock Strat neck on it. However, these guitars were apparently designed to be shorter-scale.

So can I put a full size strat neck on it or not? Surely it wouldn't affect the intonation that much as I've read that: the distance from the nut to the 12th fret is a little shorter than the strat but the distance from the 12th fret to the bridge is the same.

The mustang came in both scales at one time. So the longer scale should fit. The nut is farther away form the bridge instead of moving the bridge.
So having the nut further away from the bridge shouldn't affect the intonation / action then?
not sure about that O_o makes no sence at all lol

if it was the nut being further away then any neck would work...not the case!

Guitar : Fender CIJ Mustang and a Telecaster
Amp : 76 fender champ
Pedals : BBE green screamer, Big muff, Ibanez LU20 Pedal Tuner, boss loop pedal
The scale length is the distance from the nut to the bridge. So some mustangs came with a 24" scale neck. And some came with the usual 25.5. They didnt make a special body for each or move the bridge. The 24' scale the nut is just closer to the bridge. I put a 24.75 scale warmoth neck on a fender strat body. No intonation issues the nut is just 3/4 of an inch closer to the bridge and the frets are measured for that scale. It becomes an issue when somebody tries to put a 24 fret 25.5 scale neck on a body made for a 22 fret 25.5. Then the bridge would be in the wrong place.