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.
Other examples:
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.