If you are going to ride this bike with gears, you have to use these bosses.
Either as fixation for down tube shifters or for shifting cable adjusters.
No matter how you will do it, the paint will be damaged. Just is bit tho'. Oky, the damage is bigger with (moving) down tube shifters than with cable adjusters/stoppers, but also the adjusters will make an imprint in the paint or metal.
Only if you will ride it fixed, you don't have to use these bosses and can keep the paint quality in best state. But even then, I would cover these bosses with some kind of cap (e.g. cable adjusters without the adjusting barrels), to prevent that the rider will get serious leg injuries when scraping the legs against the (sharp) bosses.