@awapniak I had a look at the areas you mention:
Fort Hamilton: roads are marked as ‘private’, land use military on OSM. If this is a military base it seems correct that they should be excluded from citystrides (kudos for getting in!).
Seagate: it’s not clear from wikipedia whether access to those streets is open to all (no checkpoint or other access control). If it is, you could change the OSM access tag from ‘private’ to ‘permissive’ on all the streets, and hopefully these roads should be back in the next update.
Navy Yard: OSM has most roads in this area as ‘unclassified’ and not access restricted. Could you specify what you mean when you say they are off-limits?
Maybe have a look at the discussion here which is about optimising the query to import the set of roads. It sounds like you have found some interesting edge-cases that are relevant!