I'm not sure if it's the clean lineart and setting everything up so I can color it, or coloring itself 
But I'd say, from filling in the base colors 'til finishing the last highlights takes the longest.
In terms of filling in and closing gaps, Clip Studio Paint closes them pretty well if they are not tooo big. But I always go over it with the lasso fill afterwards, because the thickness of my lineart varies. So here and there doesn't fill in everything or it pixels a bit beyond.