Your last paragraph seems the much more likely explanation. It seems Trump almost certainly would have used this authority against his domestic enemies if it were actually within his practical command.
I think so too, which is disturbing in its own way. I don't want president abusing that information, but if the president is powerless and considering the NSA has already shown that it is able to outright lie to congress without consequence what hope do any of us have to change anything? Seems like they've got all the power and no one is able to keep them in check
Something you learn about large organizations if you work in one for a while is it can often be hard to make the organization do things it doesn't want to do, even if you're the top honcho of the organization.