my only thought in just using the diodes (as stated) would be that you are overloading the brake light circuit cables, possibly putting twice if not more current through them,
they may just be quality control check marks - the colour may just be whatever the person doing the check was using.
does seem strange that the toyota empire would use splodges to identify parts ;)
as you can see in pic earlier posted the markings on mine are also
3 x red splodges
and 1x white + 1x orange
and they are definetly off a 2002 SE and not the lowered ones