Wilbur is using the Planchon thing with a slight twist: anything below "sea level" is considered as not part of the area to be filled. This change allows the ocean to capture basins without too much odd filling. I keep meaning to allow selections to have a similar effect (areas outside the selection don't participate in the fill as opposed to the current technique of filling everything and then using the selection as a blend mask), but I'm a little time constrained these years.

One classic technique to the overlarge basin problem is to downcut the lowest point on the basin's edge. With a good basin-fill algorithm, it's not too bad: fill the basins in a temporary copy and then scan along the edges of the basin to find the outlet (a very slight non-flat slope in the lakes helps). Then drop the basin edge in that area by an appropriate amount and rerun the operation until the basins are a suitable size. This technique is also on my list of things to look at some year.

As I describe in the various Wilbur tutorials, I'm fond of running a process loop of basin fills to rough out the flow connectivity, white noise to rough up the flats, basin fill again to reestablish connectivity, incise flow to rough in the raw flow channels, a basic fluvial-style process to clean up the excesses of the incise flow process. The results are strangely plausible.