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 thread
(feel free to delete this if I missed it elsewhere or ... )
and oh, by the way, nice work kovidgoyal !!