The character will be better with non-proficient weapons outside of his skill than with non-proficient weapons inside of the skill...
Should it be made that the NPB also works with the same skill?
I would say no, cause then that would be giving a special rule for one skill (and possibly not the same skill for every character.
Also, please keep in mind that you are talking about a situation that is very unlikely to ever happen very often, if ever.
Only Pure Fighter types have Combat Training II, and for a character to get 12 ranks in any skill, they will have to gain 120 CP/XP above their initial 100 XP character. With 120 points, they will most likely have gotten every combat skill possible, or at least all the specialties in their primary base combat skill....
Any system will have little quirks if you go to extremes like this. It is not something to worry about in the long run. Any system can be broken if you are really trying to break it. Novus is deigned o be relatively difficult (not impossible) to break accidentally (which is the bigger worry than somebody breaking it on purpose)
In fact, most of the time, you will likely see the NPB bonus will be for the modifier to DT. The rest of the time, players will likely only use weapons that they get the full bonus in, unless you give them a situation where it is impossible to use the weapons they have full skill bonus in.
