You're speaking about "%FACTION%'s Prison" type of location.
Enemies you meet on main floors are either recon parties or strays most of the time.
Faction prisons? They live there. And are eager to defend their home.
I believe that prisons on boss floors are a side effect of having actual locations as prisons.
Which is good! Being dragged to some limbo, with a chance to lose some valuables there irreversibly, sucked.