That first jail was out in the middle of the desert, near a Mudokon encampment. That's where the Glukkons set up shop to trick the Muds in to slavery. It's not in any facility.
As to whether the two jails are the same;
the first one had wooden walls, but the jail in the
Good Ending FMV looks like it has stone walls. They look similar, but they're clearly different jails.