Well this is embarrassing but I just realized that bug now. Sorry if others have pointed it out before and I didn't notice. Turns out there should be a simple error in the code checking the number of playable characters from the guide.
The default guide, as well as the Bare Knuckle 2 (JE) and any other guides based on the default one, have a line saying "4 // Playable characters". Yep 4 characters sounds like correct in Streets of Rage 2. But... instead of 4, pancakes thinks there are 3 playable characters and that's why it disables skate collision boxes.
Make sure to change it to 5, and wherever pancake 2 is hosted, please fix that in the guides. Telling 5 playable characters pancake will assume 4 playable characters and that will fix Skate collision boxes.
Also meanwhile if anyone is going to host pk2 v1.6b somewhere, maybe I don't have the most recent guides of all, but I have guides for Bare Knuckle 2 (JE), bk2-ivex-gs update, and latest syndicate wars, in case it's useful to anyone.