These discrepancies hold true for UK and German forces as well, e.g. the German Heer sniper team and breach teams have rarity values above 0 in the Available troops section (strict rarity), but when purchased they have none.
Towed guns do get charged rarity, but less than what is advertised. In fact, this seems to be the case for every unit in the game. I cannot get any unit for the same amount it should be. It is always less, or nothing.