I would like to do some more complex transformations to AE2 patterns (create a pattern with all inputs from a collection of patterns producing a dummy item to make pattern providers respect items from other pattern providers attached to the same machine).

Implementing these transformations directly in the pattern provider would probably not be an ideal implementation.
Instead, allowing the user to copy all details about all patterns in the "9x3 modify grid" to the clipboard (e.g. in json format) along with a function to create patterns using the same format from the clipboard would allow to implement these modifications easily outside of the mod.

Unfortunately, my Java and especially Minecraft modding knowledge is not sufficient to implement this myself :(