As written, the "Custom Vehicle" trait (AToW, page 112) goes from "Choice of Stock (any I.S. Affiliation)" at +3 to "Design Own Vehicle (I.S. Technology)" at +4 with no regard to the complexity of a design (and similarly at +6 for clanners). I propose removing that +4 (+6) level and replacing it with a point cost for the Field Refit Class (CO, pages 211-212) that can be added on top as follows:
Class A: +0 (Armor tweaks, Equipment removals)
Class B: +1 (Equipment replacements or facing changes)
Class C: +2 (Equipment additions or relocations, engine HS changes)
Class D: +3 (Multi-location Equipment, CASE addition, Gyro or Turret changes)
Class E: +4 (Cockpit or Engine changes)
Class F: +5 (Internal Structure or Myomer changes, Turret addition, changing fixed equipment on an Omni)
Refit Kits (CO, page 212) are obviated in this case by the "Choice of Stock" options prior to applying customization.