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The SENSORY FOCUS and HYBRIDS Adaptations both specify Primary "tile", not "site", so are the following tiles still eligible for these Adaptations: I think you are correct; primary tiles are those tiles that have 'primary' written on the back site. What site they end up on is irrelevant.
Q1: A Primary Tile that was placed on a Secondary Site due to SPECIAL DISCOVERY? [I am going with YES]
Q2: An Alien Tile that was placed on a Secondary Site due to a SPECIAL DISCOVERY pulling an ALIEN CULTURE CONTACT from the Primary Discovery pile? [I am going with NO]
Q3: An Alien Tile that was placed on a Primary Site due to ALIEN CULTURE CONTACT? [I am going with NO]
I suppose another way of asking this question is which of these is considered a Primary tile?
1. Only tiles with Primary Site on one side (like Q1).
2. Any tile that ended up on map due to a Primary tile (like Q2).
3. Any tile on a Primary Site (like Q3).