There's a huge difference between being able to operate the systems on a complex aircraft (or spacecraft, in this case), and knowing the systems well enough to be able to handle emergencies effectively. The former just requires you to have a basic understanding of which controls do what, the latter requires you to have a deep understanding of the guts (both hardware and software) behind the panel so that you can troubleshoot effectively. To give one example, I would imagine that the details of space navigation systems are also off-limits (you could use such knowledge to build an ICBM guidance system), so you could teach people the basics of using the nav system on a space ship, but they would probably need security clearances before you could teach them how the nav system works under the hood. Going back to the propulsion system example, you could give anybody a basic explanation of how it works, but security clearances would probably be required for the level of understanding a pilot would need in case of emergencies.

The main concern driving these restrictions is proliferation. Just letting someone operate it is not a significant proliferation risk--you just have to vett the individual well enough to be sure he won't try to land it in Mexico.

Similarly, using it as a suicide weapon is also a minor concern because similar thorough vetting will weed out anyone inclined to deliberately crash it into a major population center.

Proliferation is much tougher to control, because once a foreign national returns to his home country, we have no recourse if he decides to start sharing what he learned. It's easy to screen out people who would do extreme things like steal a space ship or use it as a suicide weapon, much harder to be sure that someone will keep unenforceable promises not to tell secrets.

The tour was arranged for a group of students, myself among them. Some of my classmates were foreign nationals and they weren't allowed to come.