They're a little bit of both; IIRC the designers didn't know how long the Scourge would persist and people would need to stay in the kaers, but they knew it was a long time. So the kaers were designed to house people for centuries as fortified and magically warded subterranean settlements. As much as possible, they were self-contained and self-sufficient. The Fallout Vault comparison is apt, except that to the best of my knowledge they weren't part of an elaborate crackpot eugenics experiment. In any case, given all the underground city talk I thought kaers might be a good potential source of fantasy setting inspiration.