I've tested it on a locally forked version of your mod - I does work in packed mod, I can send you a video or a save file (or you can just try it out yourself on 1.2.3 version of Recipe Combinator).
And it's not really an assembly machine it's speed is set to almost zero - no one would be able to craft anything with it, it's just implemented as assembly machine but can't be used as one.
AND this change won't allow any other assembly-machines inside Compact circuits processor - only ones that are registered with mods specifically with your API - you use that "forbidden_prototypes" solely for other mods' calls and not for actual placing any entity (for that you have a separate check - please review your code).
"There are already in the description the steps to support properly any kind of combinators." - and I've done thouse steps, but to integrate it already. It just can't be placed because of that restriction.