My apologies for reanimating a months-old thread, but I happened upon this while searching for something else.
I don’t know about the “undecorated” setting–I don’t think that I’ve tried it, myself–but I’d like to confirm the issue of a custom prc file being largely ignored, including the “win-size” variable mentioned by Wezu above: as I recall, I’ve experienced similar issues. A previous post of mine on the topic can be found here, I believe.
(Thus far, my only solution has been to set such things manually, after the program has started.)