I would think it would also make sense to have forces outside and above ground that patrol and defend the base. Wouldn't it make sense to have a base defense mission have two parts - one that is above ground outside with a landed UFO, and a second that is the interior of the base if the aliens get that far?
After all, in various versions of X-COM/UFO and the inspired re-makes, some alien base assault missions have two parts, one that is outside where the goal is to get to the entrance and get inside, and the second map where everything takes place inside.
I don't claim to be an expert, but with regards to military installations, even ones that don't disclose what they do there, as far as I know many have fences, walls, etc., outside, or at least some kind of exterior defenses and agents, officers, or soldiers, etc. that patrol the area and control and monitor anything that approaches the place. Heck, even special places in urban areas have armed security and special police forces that patrol.
I actually have a little bit of experience going to such places and know a few things about this, partly from my last job, and I can't elaborate on too many details but I'll say that I don't know of any such installations or real-life bases where you aren't normally detected , watched, and have to pass through a good deal of checkpoints and outer patrols before you even get close to the place, and then pass through more security getting inside.