I've never seen a similar layout. When I do a fiberglass pan/shower, rarely, I would bring the shower backing, Duroc or similar down to within 1/8-3/16" of the base. Nominally you would be about 1-2" off the floor. Use thinset to fill all the voids and corners. Then you can tile, leaving another gap, similar to what you have. I usually grout everything except the bottom gap. I finish with a good silicone caulk, base gap and wall corners. Was there any wall covering? The last one I did had a preformed base with a 1" flange. Purple board on the walls, screwed the base to the wall studs, tiled as above.
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