From my understanding rubbing compound is an abrasive. It works by finely sanding your paint down which removes any blemish.
You want to apply wax afterwards to reapply protection over the area. Be careful leaving it on too long or using too much as it will take the paint off.
I think the difference of the two products is the strength of the cutting agents. Like the difference in 1200 grit and 400 grit sandpaper
The suggestion of using a clay bar is also good. Way less abrasive.
These rubbing compounds are generally made for machine use, so made for use with a commercial buffer or random orbit buffer. When used on a soft cloth by hand there’s very little paint removal. There is some of course but very little when compared to the thickness of the clear coat. The paint is subject to surface wear anyway, every time one drives through dust, when the car in front picks up road sand and you drive through it, etc. You are right about the differences in the aggression of the compounds and polishes. On the other hand he’ll stop when the mark is gone so a fine polish will be less aggressive but he’ll rub longer. The microscopic surface of the paint will be smoother if he uses a fine, nonaggressive, polish.
As far as rubbing out little marks, you should be able to do it for the life of the car, there’s not much chance of significantly thinning the paint. When he takes it in for that $250 mark removal, they are going to use a machine, they’ll probably do the whole door, they’ll remove much more of the clear than he will by hand.
About waxing... Something should be applied to the paint, whether wax or one of the newer polymers. You want something on the paint between the paint and road grime, acid rain, tar, bird droppings, UV sunlight, and dried bug splatters. Some of that stuff is pretty harmful to paint. So if there is nothing on your paint, you might think about applying something. Modern non wax finishes can be applied and wiped off very quickly and easily. The old days of the carnuba waxes and the all afternoon workout, applying and then rubbing if off are pretty much behind us. Some people still do it, though.
Clay... if you haven’t used it, you are in for a treat. You start with it after you wash the car, you spray a little of the provided lubricated spray and wipe the clay bar across the surface. If you run your hand across the paint before and after the clay, it’s pretty impressive. Before, the hand sort of drags on the paint. After, it is slick as a whistle. The clay picks up the remaining surface contaminants and leaves smooth pristine paint. You periodically knead the bar to expose new clay. You have to be careful, though. If you drop the clay bar, that clay bar is done. It picks up grit from the ground and the grit will damage paint. You cannot clean all the grit from the clay, nor do you want to try. Clay is excellent for stubborn dried bug residues and also those stubborn dots of hardened black road tar.
All this is opinion, anyone with better info is invited to jump right in. There’s a site, Griot’s Garage that has lots of information for anyone interested.