I think you are actually right, it doesn't really matter as you only go on when a seat is available . And on my last company a ZED ticket was even more expensive than a normal ticket, if you booked that a bit in advance. So the company could probably even make some money on it.
But one reason might be, that most LCCs are not IATA members, which isn't a requirement for Staff travel, but it seems like most IATA members have ZED/ID90 non members don't.