I am not sure either how far fetched it is. But what I imagine is that they are using the hidden vectors to calculate the intersection of lines and delete that segment.
Open Toonz creates invisible vector lines as you draw in raster and then can make operations on it as tohma seems to be taking advantage off since it was forked from it.
As of now I think krita would have to create a filter to analyze pixels that is meh in results since pixels are pixels. I made a brush engine suggestion in order to help with this kind of operation. Maybe you would like it too.