As new user to Calibre I was investigating this subject (but because I wanted it larger, hihi) ... for those looking into it in future:
for me worked just to run E-book viewer from start menu (ie. just run it empty), check "Remember window size" in preferences (along with other settings I wanted as defaults), and then close it. It worked same way as if "setting defaults" function. Hinted to do this by sherman in this
(feel free to delete this if I missed it elsewhere or ... )
and oh, by the way, nice work kovidgoyal !!