Yea, it looks like it has to be that way. I really can't find away around it. Just so close and just can't get this one last thing kind of bites. Anyways, my last thought to try is add a tag to the chosen skill (somehow) and then try
foreach thing in BaseSkill where "Helper.ClassSkill | Custom.FGMP3ModTr"
eachpick.field[BonTrait].value += 1
nexteach
foreach thing in BaseSkill where "Helper.ClassSkill | Custom.FGMP3ModTr"
eachpick.field[BonTrait].value += 1
nexteach