How to protect sill plate from water when slab is bigger than the structure sitting on it

This is a tough one. There is no easy way to remedy your problem. The best way would be to remove and replace the tiles properly. If in fact the tiles are real marble, you can grind them to create the proper angle and slowly refinish the surface by stepping down grits and finally getting to a wet polish grit of 2400. That is actually impracticable for a DIY if you don't have the equipment and materials to do it. If it were me, I'd remove a couple of tiles and reset them to fix your drainage problem. A couple of hacks with a hammer, scrape off some of the thinset, replace the tiles with a little premix thinset, regrout, wait a couple of days, seal the grout and your done. The actual labor time may be only a couple of hours, even though you have to wait a bit to use the shower again.

Drill a hole, or a recess, into the bottom plate of the prefab wall, so the bolts holding the sill plate to the concrete just slide right in/through.

Or, drill a similar recess into the sill plate, recess the nut into the sill plate (probably with a washer to spread the load over the thinner wood), and grind/cut the bolt off level with the top of the plate.

Whatever you do, make sure this doesn't compromise the structural integrity of the sill plate or wall (shouldn't) or introduce any potential for leaks or collected water inside the recesses or holes (again, shouldn't, provided the skin of the shed remains watertight and you're not saturating the inside with a hose on a regular basis)