I largely agree with @dragoon500ly.
Permanent bases that were expected to interact with the public would have short-term/emergency habitation in the base but would expect to build and use surface buildings as soon as practical.
Bases not expected to work with the public but not considered as high value targets would spend longer underground and when/if they built external housing it would need a secure but discrete connection to the base. Perhaps build a hotel/inn with a secret tunnel in the basement.
High value targets like Prime Base and the Regional Command Bases would just be underground for the duration of the Project. Precise location would be tightly controlled and staff rotated out as necessary, but too dangerous to have an external structure.
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