Hello Drover

The Glycerine acts like a Sponge to methanol.
If the reaction has stopped you have reached equalibrum with your chemicals, some is in the biodiesel and some is in the glycerine and no amount of mixing will significantly improve the reaction.
The methanol would much rather be with the glycerine than with the biodiesel because they are both alcohols.

If you leave the glycerine layer and add more methoxide, about 2/3 of the added methanol will be "Sponged" up in the glycerine layer and effectivly removed from the reaction leaving about 1/3 for the reaction.
If you remove the glycerine layer then all of the added methanol will initially be available for the reaction.
That is why in a 2 stage base/base method you can use substantially less methanol overall.