Filling a line art create a low opacity line outside of the selected area.

It sounds like you are doing this on a single layer.  We can only guess at the set up here, but if the pale yellow is on one layer and you need to fill the gap between, then use a new layer further down the stack, and paint behind the pale yellow.  Or am I misunderstanding?

@Scarslatte what zoom level are you at? How does it look when you are at 100%