There's a setting to turn off undiscovered map markers. Perhaps you have this set and rune doesn't. The default is to show them.
Ah ok. I just realized that I can scroll down and see more options in the HUD configuration menu that I wasn't aware of. Cool.. it looks like I can remove those button prompts after all.
As far as the map markers though, I only see an option to toggle them on the mini map. I thought rune was talking about the main map. I wouldn't know what the mini-map shows because that was the first thing I disabled.
I have to give CDP some major props for allowing the HUD to be this configurable. I hope other developers are taking notes.