The reason the conversion and the Gibson don't line up is because the 12th fret is in a different location then the 12th on the gibson. Think of it in reverse the bridge is in a different location on a gibson and a warmoth. The nut can be moved up down anyway you want during manufacturing of the neck but the bridge will alls be in the same place so you take you measurement from there instead of the nut. the bridge on a 25 in scale sits slightly further back so if you just shorten the neck you will be out of intonation. The only constant is the bridge so you measure half the distance from there and set the frets accordingly and it my mind at least it would make sense that they don't line up with a gibson.
Not sure if I explained that right
Not sure if I explained that right