I just finished my custom MBM1 kit a few days ago and noticed there are some serious intonation problems, I had to move the saddles all the way toward the neck and the intonation was still too flat at the higher octaves. So I measured the scale length (which was supposed to be 25.5" for my request) and It seems that it's missing 5mm from the 12th fret to the saddles.
I really hope that I got it wrong 'cause if this is the case I understand that I need to redrill the holes for the bridge. I ordered a replacement for the bridge, a wilkinson roller bridge that maybe will give me more range with the saddles, but maybe someone here got another creative idea that will not involve damaging the finish. Needless to say, this is extremely frustrating, I planned it to be may main guitar and except for the intonation problem it really turned out as I wanted, so any help will be appreciated.

12.75" from nut to 12th fret seems to be spot on:
Click image for larger version.  Name: WhatsApp Image 2021-07-20 at 10.39.05.jpeg  Views: 165  Size: 257.9 KB  ID: 41070

From the 12th fret to the bridge:
Click image for larger version.  Name: WhatsApp Image 2021-07-20 at 10.39.05 (1).jpeg  Views: 171  Size: 343.7 KB  ID: 41071

Demonstration of the issue:
https://www.youtube.com/watch?v=k99O...hannel=SeitanY