Some cars, depending on the colour, use white primer, often bright coloured cars such as reds, blues or yellows so it could be that that you're seeing...
General rule of thumb is if you can catch your finger nail in the scratch then its too deep to machine polish out.
A machine polish/rotary/orbital etc is usually a variable speed machine that can use a different variety of size and type of heads. You use a cutting agents with these heads to remove the marks - cutting agents vary in the depth of "cut" they give to the paint, some will cut deeper than others and some are used for final stage polishing. Cutting means the amount of paint the machine and agent will remove, don't worry, it's microscopic layers. Paint thickness is measured in Microns, a decent cut will remove a few layers but not all unless you're being a complete idiot with it.