Regarding your first question:
You cannot 'flip' the word order as you suggest. You could say:
the herein-contained mutual agreement ...
The reason is that 'herein-contained' has become a compound adjective describing the mutual agreement, rather than a verb and adverb as it is in the first example. "The" goes before the adjective in such cases (eg. "the red bus", etc).
Regarding your second question:
As user 307254 said, "contained" looks like the simple past, but it isn't. It is a participle being used to form a passive construction.
It may help you to add a couple of implied words which have been excluded.
the mutual agreements [which are] contained herein.
It is a very common construction, and has no sense of the past at all. It can be used with auxilliary verbs to create any sense of time you like.
The cat is locked in its cage.
The cat will be locked in its cage.
The cat was locked in its cage.
The cat had been locked in its cage.