There are some items I would rather not go into the reagent bank automatically, eg Felwort Seed. Would it be possible to add an ignore list for the auto-deposit ?

Ah. I thought it was part of the addon. I will send the suggestion to Blizzard ;-)

Auto-deposit is a Blizzard-provided black box feature. It's not possible to choose what is deposited, unless the entire functionality is replaced by the addon. At this point, doing so is not planned as far as I know. However, you can and should report this request directly to Blizzard.

While you're at it, how about getting Blizzard to auto-deposit to profession bags before the reagent bag, when present?