Sanding a polished top is all about getting the finish flat without sanding through to the timber. Sanding through means you lose colour and you get dull spots where there is less finish.
If you think you can do it, use the ROS, otherwise hand sand with a cork block.
With regard to the filler, wood flour works but it isn't black. This is why I suggested charcoal instead. You can fill it and proceed with coating. The wood flour you will have to colour.
I also don't recommend using different classes of coating in the one job. Doing it all with urethane means you are not risking incompatibility between coats. Plenty of guys use shellac as a silver bullet however. The final decision is yours. Cheers