It could be possible that they were recycled... but i doubt it. It is likely that stages are set in the same place. Those are good examples of cross reference, that you mentioned.

"Cross the checkpoint" from Tenchu1, was a border between Gohda territory and another land... and the caves/forest, was where Ayama was captured by Gu. It also mentions 'the bear' somewhere else in Fatal shadows. Something about it recognising the scent of Ayama and wanting revenge for killing it's parent or something? Can anyone remember this?