It doesn't matter what the LSA *thinks* , they are wrong and at fault.
It's not the fine print either, it's quite obvious and, not only that, it's standard procedure and there is not excuse for no following it.
There are times, and this is certainly one, where being reasonable takes persistence over procedures and the manual. That is what an intelligent person would conclude.
No where else in Amtrak, is two or more people assigned to sit in one seat. Not even in lower priced coach. One seat = one person is the rule-of-thumb. And anyone looking at a roomette would see simply two seats (and not all that wide of a seat).
There is no excuse to follow something you know is dead-set wrong. I applaud the LSA for taking the high road and using his/her brain. More people should do that.