I'm not 100% sure if this is a bug or intended, but right now the following settings allows you to mine any block with your bare hands and get the block drop.

    # If blocks are mineable without the correct tool.
    doBlocksMineWithoutCorrectTool = true

    # If blocks drop their items without the correct tool.
    doBlocksDropWithoutCorrectTool = true

I've already pinpointed the potential issue as being here, where the result is OR'd (||) with the harvest check code instead of AND'd (&&).

Yeah, that config option does what it says on the tin. The || behavior is intentional too, as it's intending to widen vanilla's harvest check - if vanilla's harvest check passes, it needs to harvest because NTP's behavior will almost always fail. Or at least, that's the theory.