The mortar bed and plywood are sitting on concrete?

No, they’re both supported by the floor joists, which might be sitting on a poured concrete wall that runs underneath the bathroom. It’s a little hard to see exactly what’s going on under the floor, visibility isn’t great under the bathroom from the basement. Filling in the plywood section with mortar would require building out some sort of form to keep it from running into the basement.

The mortar seems pretty robust. The only way I’d be able to get it out would probably be the rotary hammer or a big sledge hammer or something. Ideally I’d like to just put SLC down as-is, I just want to make sure the cracks and divots won’t cause any problems with that. The floor transitions to hardwood, and currently the bathroom subfloor sits about a 1/2" lower than the hardwood, so I’m hoping that’s enough to fit a layer of SLC, ditra, and tile. I would like it to be flush, but I’m not super concerned if the bathroom floor ends up a tad taller.

I appreciate the feedback though, thank you!