Barry-In the second pic what is that dark orange brown marking that looks like it goes right across the grout line??
I agree with Fred- Onyx is very soft as well and sensitive but polishes well.
How is the install-check the lippage.
Are any of the pitting deep enough to need filling?
Some marine toilets use disinfectants to treat waste before discharging. So the pitting probably resulted from the chemicals in the backup mess on the floor.
I would treat that area with either a sandpaper or electroplated pads like AT genesis or similar.
Be mindful of dipping the area and keep the tools flat.
Then I would assess the surface and see if any filling is required.
If so I would use a CA gel and accelerator to fill-that should give you the best quality fill.
Another product that will give you a excellent result is Bonstone Dymond a 2 part urethane which will give you water clear fills. This product is rated for exterior and performs well in wet areas.
Once you have repaired the area use traditional diamonds 220 to 800 (making sure you take care of the picture frames) then polish.
If your not used to onyx use a compound that may be easier to MPC from SCC or MB-22.
MB-22 works great on Onyx.
Its my opinion spot repairs can take as much time as doing the whole bathroom floor.
Just blend out your polishing- you will be fine.-If your not sure grab a piece of onyx from a fabricator and practice on it.