Both warmoth 25.5" and 24.75" scale necks are designed to mount to regular Fender scale bodies. The Gibson looking bodies share this geometry. You should be able to stick either scale on a body and it work. The 7/8" scale and 24" scale (note unusual different context uses of the word scale there) bodies are different, and have a different bridge to neck pocket distance.
Tune-o-matics do require a neck angle, and certain bodies from Warmoth come with it built in. Also I believe ordering a non-recessed TOM triggers the required neck angle in your order. I just went through this because I wanted a 24.75" scale guitar with Zero neck angle (because I hate Gibson ergos). But if that was the problem it would probably show up in absurd action issues, not intonation. Lots and lots of people have Warmoth LP bodies with Warmoth 25.5 necks. If the body is someone elses, then its possible it was built as a bolt on with a different bridge to neck pocket distance.