I have a games\bg folder for BG1 that I use for Tutu. I tried running it to test this theory in-game, but since the baldur.ini is set up to do Tutu stuff, it didn't work.
So I copied it to games\bg1 and restored all my backed up virgin files into that folder. montar2.cre doesn't exist in override, and in-game he has 2 profs in small swords and missile weapons, as stated above. He also has 'em in his .cre.
My theory is that when Tutu removes all the NPC's proficiencies because they do in fact show up in BG2 if they exist, it doesn't remove them afterwards. Mystery... SOLVED. Go go TeamDing0Fain.
Just checked montar2.cre on my install, and nadda. Although I have BD installed, but... why the heck would that affect anything? Do you have TOS, or the 6-CD original?