During my 2P coop run we had a moment where we threw the boss on the ground and then did double thunder on top of him to absolutely steamroll him.

Moment located at:

Thinking this might be usable against a few bosses that hit the ground for a period of time. Likely not on Fungus or Diablo, but maybe some of the others. Double thunder is also very good against the swinging miniboss before Moai.

That's completely true. In fact during me and Ritah run we managed to do it on some bosses as well. However, the throw loop used on single player runs is faster.

Nice, I couldnt figure out a super consistent method for actually doing it with my partner though, I am not sure if double thunder you have to be right on top of eachother doing the same punch/kick move to activate.

One boss Id really like to figure out how to use it against is the Robo-ape boss

If I remember right, both players have to mash punch button at the same time for it to work.