So I'm trying to edit the nav mesh for Ghost Town to create sentry spots for engineers, but even after marking/unmarking areas and using 'tf_mark SENTRY_SPOT' numerous times the engineer bots don't move or teleport to any of the spots. What am I doing wrong?
Engineerbots in MvM don't care about the SENTRY_SPOT mark at all, they're programmed to build their nests based on building hints that are placed into the map via Hammer. You can even find out how that works, here.
As Fillmore said. In order to add proper support for engie bots in Ghost Town, you would need to make your own modified version of the map with added bot_hint_engineer_nest, bot_hint_sentrygun, and bot_hint_teleporter_exit entities.