Some of our XRLs (remote bases) will be pet friendly, yet designed to contain pets to the designed environment, by keeping the wilds outside relatively free of alien species.
"Leave it as you found it" is the prime directive in many a protected wilderness.
Pet owners have long used plastic tubing to vector hamsters into harmless holding patterns. Dogs may also be coaxed into traversing short distances through tunnels, Dachshunds especially.
In other words, structures needn't directly connect in order to provide safe passage to controlled species, by means of appropriately sized tunnels. Humans needn't be restricted in this way, having trained themselves to obey the appropriate rules even when set at liberty.
Given RFID, some systems will offer fancier control paneling for monitoring pet whereabouts, whereas other communities might consider this overkill, an invasion of privacy, and opt for stronger training instead (like our pets don't "get stuck" thank you very much -- or if they do it's none of your business).