Originally posted by Faceplant8:

Snip

Have you tried entering the same crypt in each world? You can actually test with a single world. Enter a crypt, explore a bit, leave, rollback to a previous backup and get into the same crypt. The layout will be different. Like you said "I tried it".

Yes a lot of the world will be identical with the same seed, but there are parts that use a random parameter on the fly when generating areas as they get discovered.