Able to / good way to cover / handle cleanout in the floor
I would fit your flooring neatly around the clean-out rim, and then screw down a stainless steel cover plate that laps onto the flooring. You can run the screw right into the cleanout plug.

The clean-out is presumably for your main sewer line, which probably runs under the floor and out to the street or septic system. If you ever have a backup you'll kick yourself if you had covered it up.