It sounds like, once the separate universes of DC and MK start to merge together, different places become mixed together too. Here's some similar places that could mix together easily:

- Gotham City and The Street/Rooftop/Bank/etc arenas in MK3
- Shang Tsung's Island and Themyscira Island (Wonder Woman's Paradise Island)
- Outworld and Apokolips
- Superman Statues all over Metropolis / Warrior Shrine from MK1
- Lin Kuei temples are similar to some places Bruce Wayne trained prior to becoming Batman
- Arkham Asylum / Dark Prison
- MK's Elder Gods stage / Oa - from Green Lantern, where the Guardians of the Universe watch over and make sure everything's OK (Note: they seem to be doing a lousy job in both universes).
- Living Forest / I don't know what the DC equivalent is, but this is Poison Ivy's dream come true!

Can anyone think of some more?

On an unrelated note: Could the U.S. Special Forces be forced to report to President Lex Luthor!?