To the best of my knowledge, purely as a player:
On the proficiencies, you only get one specific weapon per feat spent. A level in Fighter should net you either all martial weapon proficiency feats, or at least an equivalent feat that. If you equip the weapon and no attack penalty icon appears beside your portrait, you're set.
On the one-handed two-handed weapons, it's a necessary workaround to allow wielding the weapons as one-handers. Large races can effortlessly wield two-handed weapons intended for medium characters as one-handed weapons - but since the official content never included any large player races, the engine isn't equipped to handle such content. Since the nwnprc pack includes both races and feats that allow that, the current workaround was implemented, with all weapons assigned as able to be equipped in one hand.
