Ok, the best solution I found for this is to do it as is done in the quadprog package (ver 1.5-5). Here is what the relevant parts of the src/Makevars file look like:
mypackage_FFLAGS = $(FPICFLAGS) $(SHLIB_FFLAGS)
all: $(SHLIB)
Babar.o: Babar.f
$(F77) $(mypackage_FFLAGS) -O1 -pipe -g -c -o Babar.o Babar.f
So, for example when you send the package to the win-builder here is what the compiler output looks like (confirming that this solution does indeed work):
gfortran -O1 -pipe -g -c -o Babar.o Babar.f