I’ve noticed what is almost certainly the same behavior. The size file in your applications data folder is supposed to remember window size from last closure. You can delete the file, regardless of whether the application is open or not. The next time you close the app, the file is recreated.
If there is no size file when the app is opened, on my 21" iMac, it opens at nearly full screen (allowing only space for the dock). If closed without window adjustment, it reopens at the same large size. But if any adjustment to the window is made before closing, it reopens next time with a centered window of moderate size. I can’t be sure, but your screen shot looks like you have the same size window (in pixel terms) displayed on a larger background. So your overall result is a window that seems smaller than mine due to monitor differences. For me, it is a workable size. I can see that for you it might not be not.
At any rate, the program is not working as described and intended, so I am elevating this to bug status. To be clear, @lubos, on Macs, the program is picking up the fact that the default window has been changed, but does not seem to store and recover the actual window size or location.