There's no link to the DoPostSuccess method which increases num of unique upgrades. Most upgrades link to this method via StopUpgrade except for water trough (direct link) and juice keg.
Since there was no fix to this issue (and I don't know how to write script mods) I exported my sim (after autopilot upgrade), changed one of the 0x29* (autopilot) characters to 0x28* (auto refill), put her back and upgraded another helm. Warning: Messing around here may lead to a household which can't be imported anymore!
*0x28 and 0x29 show up as ( and ) in notepad++