Maybe I don't understand problem, but it looks like you want sprite to have custom per-pixel collision mask, right?
In Image Editor you'll see "Colision Mask" button (second from right on upper tool panel), which allows you edit... um, collision mask. (But I guess you already know about that cause it looks like you already edited mask)
Just copy your red collision box in every frame when you in collision mask mode (image canvas will be outlined with red in this mode).
Right now your collision mask is empty, that's why sprite falls through the floor in per-pixel mode.
Sorry if u can't understand something due to my poor English or if I did't understand what you want