1.) The millett is just to hold the soil. The point is buying time to get in sync with the proper timing of fish stocking per #3 above.
2.) Rotenone would be applied prior to filling the pond. It can only be applied by a certified person so I'm assuming they'll do it in accordance with regulations. Once the stocked fish get established the native fish incoming upstream will always be on the short-side rather than the opposite. If the native fish get established in the pond prior to the stockers, the stockers will be playing catch-up.
I'm not the expert - just doing a lot of reading. Read at least the sources listed above, before questioning me because I can't answer. Just refute the information contained therein.