They seem to be short, unnecessary segments. The collectibles also seem meaningless, unless you want some lore.
I haven't finished the game, but I'm about halfway through and I've only been forced out of the Animus twice. You can leave anytime you like by hitting up on the d-pad when in the menus, but no thanks.
And as far as I can tell, there are no trophies for anything related to those segments, other than progressing through the story.
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