I don't claim to know all about Vanagons but I think that the low water
level/overheat light blinks mainly to show you that the bulb is not burnt out
just like why the oxygen sensor light and oil pressure light also come on when
you first turn the key and then goes off after the van is up and running.  I
always crank my van right up with no problems (this comes from a guy who is
used to waiting for lights to go out in all of his other diesel vehicles which
have been pretty much all he ever owned before he bought his first Vanagon).
So wait for the light if you want, but you don't need to wait for the light.
Ken Wilford
John 3:16