Yes, that is true - the non military guest can not be checked in and staying at the hotel when the military sponsor is not there. The way I understood the question was that the sponsor would already be checked in, but just out at the parks when they got there. They were wondering if he would have to come back from the parks to check them in. The answer is no, he should not have to. We have done this several times. As long as the military sponsor is already checked in, there is a form they can fill out to give permission for their guest to check in without them being physically present at the check in desk, but the military sponsor does have to already be checked into the hotel. And no - the guest can not stay longer than the military person. They have to check out when the military person does.
It is correct, though, that the military person does have to be physically present at the ticket counter to show his/her ID card in order for the non-military guest to purchase their tickets at SOG.