The 24.75 conversion neck that both Warmoth and Musikraft sell are designed to work on 22 fret bodies and will intonate properly.
24 frets is an entirely different ball game. Warmoth has published the methodology for how the 24 fret, 24.75" '7/8 Warhead' necks and bodies are designed. Musikraft specifically says that you will need a 24 fret body for their 24 fret necks to work but they also do not publish how they derived the 24 fret neck such that it could be compared easily to verify the methodology is compatible or even in the range of compatibility.
Since I have recently gone down this rabbit hole for myself, I can provide some of my findings in this matter.
Wamoth says that the 7/8 Warhead design is a a standard Fender style neck shaft with 24 frets overlaid on the fretboard with an overhang to make the 24th fret fit. This mean that the measurement from the face of the nut to the butt should be about 18-27/64" then the overhang is beyond that by a 1/4" of an inch or so. This is the measurement that will need to be confirmed with Musikraft. HOWEVER this only applies to the 7/8 warhead neck and body not any of the other offerings from Warmoth or Muiskraft.
Hopefully this helps.
PS to answer the question in the thread title, Yes 3/8" is way more than enough to matter for intonation.