That's not my experience. My experience is that CMD-W, open in doc has been opening to the corrected size. I have now tried it well over 200x just because others were having issues. It's beginning to look like not everyone's set up is exhibiting the same behavior. For me, regardless of whether I'm hitting the red x in the window or CMD-W to close outlook, opening it back up in the dock opens to the corrected size.
I went so far as to make the window small, CMD-Q to set the window size, re-opening it to ensure that it comes up as the small size, made it large, CMD-Q to set the window size, opening it again to ensure that it was the large size followed by 50x of CMD-W and red x to close outlook. Each time, the window opens to the large size.
If it helps, I'm running a mid 2015 MBP 15" running El Capitan 10.11.2 and Outlook 15.17.1.
I had this version of outlook running on a 2011 MBP 15" running Yosemite and never had this issue. It's only when I went to the new laptop that this issue started popping up.