In my eyes Tool have always been a prog band, which is why I thought the Meshuggah comparison they made was strange. They're just so far removed from prog than most of the other bands out there, so that's where the uncertainty comes from. They haven't done anything that paints them as a metal band other than use lower keys and distorted guitars, which is something many non-metal bands are guilty of. What they have done is taken complicated/busy music and made it listenable/enjoyable for people who can't follow everything that's going on, and that might be how they're influencing other bands.
For the record, Tool's okay, I have to be in the right mood to listen to them.