The 5th prototype going back to test trench-style exhausts with DSI intakes is strange. I would have thought they'd eliminated the trench-style exhausts after the 2nd/3rd/4th prototypes all ditched them. If there was a time to test trench+DSI, it would have been the 3rd prototype (after the 2nd tested 2D TVC + DSI). Hopefully we won't see Caret-style intakes return, as much as I like them aesthetically.
Its possible the programme isn't as far along as we think if they're still testing major changes like this, or perhaps they're testing for a new variant.
I would be cautious in assuming the exhausts are the exact same as in prototype 1 -- specifically, I would hesitate to call them "going back to". It may well be a new configuration of a trench style exhaust, or something else entirely.
As for the changes in the aircraft between prototypes; I read it as they have specific parts of the aircraft that are well circumscribed that they're willing to try different things for (given the project itself is somewhat unprecedented), but the rest of the aircraft should be proceeding along a common line of development and progress.

