I don't know what takes more time; to separate the layers, or to color the lineart as one whole layer. I tried to color the lineart as one layer before, but if the character has a lot of colors, it's kinda hard because you have to watch exactly where you color and mustn't do mistakes on these thin lines. So separating layers is recommended.
well when i do a base color for lineart I use this handy little brush mode called behind. every time I paint a color on a layer it will essentially go behind whatever was placed down before basically not over coloring anything you have already colored. lol i hope that makes sense. will work essentially the same, and that way you avoid the many different lineart layers. but your way does get more exact.