First take very accurate measurements of the rough-ins and draw a proper diagram showing each of them in relation to the nearest walls.
Cut each out below ground level and then fill with floor leveler. If during the cutting process you are opening or exposes a PVC pipe, cap it before the floor leveler.
The other option is to try to hide them in walls but looking at yours, probably won't work.
The "pipes" here were never expected to be used as-is. Sometimes maybe but not normally. So you cutting them will have little to no damage to future use. If people know where they are at and the pipes are in good workable condition under your flooring that is 98% of it.