Waze can’t know your level of access. So, the idea is to assume that your level of access is barely sufficient for where have asked to go, and no more.
If you are outside the base, and you want to go somewhere else outside the base, Waze assumes you do not have access to the base and routes you around it.
If you are inside the base, but there is a facility within the base to which you don’t have access, again, Waze will assume you don’t have access to that facility unless you ask specifically to go there. (Note that very small installations/neighborhoods are often modeled with all private roads rather than with gates, and nested levels of access are not possible with that approach.)
I have never used the “add a stop” feature in the Waze app, but I think that’s the only way you could accomplish your goal. You’d tell Waze you want to make a stop at the base on your way somewhere else outside the base. Waze would route you to your stop, then onward.