I suspect that square hole is to allow you to put in a P-trap for a shower or tub. Have you dug down any into the sand to see whether there is one hidden there, or if you have a straight run to the wall?

Based on what you can see in the picture, that seems to be an odd location for a tub or shower. The end of a tub would be too close to the vanity on the right side wall, and the window would make it impossible for it to be a shower stall.

Its common for the rough-in for a shower or floor drain to have a fairly large diameter hole around the drain, since this provides space to install the P-trap and also allows some flexibility in the final location. However, if its a P-trap, that vertical pipe farther from the wall should be a vent, which has to go up into the wall. Yours is in the middle of the floor, unless that's just a can sitting on the floor.

Can you take some pictures from farther back that show the overall layout of the room. For example, where is the closet flange for the commode? Could that extra drain have been for a utility sink?

Bruce