Dark souls is a game that does this insanely well- everything is roughly rendered to scale so if you were to drop a soul mass in blighttown, you could see that soul mass from fire link shrine
Which if you dont know what that means, imagine being able to see a rupee at the top of hyrule castle...
The sandship from skyward sword
All the other dungeons have enough overworld space to be feasible but the sandship is so tiny
I think wind wakers dungeons are scaled pretty well
Houses in video games in general are always requiring some level of suspension of disbelief