I think that most conspiracists have developed a thinking pattern from popular media portrayals of conspiracies. While one can always find some way of rationalizing "they wanna make giant killer bats, OK?" in the script, it doesn't have to be a particularly strong reason. They're the bad guys, and they're evil. They do these things because they're evil. That's all you really need to know.
So, we see Patrick trying desperately to find reasons to justify faking the Apollo missions. Um, oh, he knows, it's to establish a space-based missile platform! When it's pointed out to him that such a setup would be inferior to systems that we do know about, he shrugs, and insists that it would work as part of such a system, so therefore it *must* be part of the system. Sort of an "if it can be done, we will do it, even if there's not much point."