My understanding of what is happening now is that the initial window size is determined by what is required so that things fit. For most people, having the Gear Changer as a tab was what determined a size that was unfortunately too large for some of us.
My plan, subject to revision, is to create new configuration variables for height and width. On start up, if they are set then they are used. Otherwise it behaves as it does now. On shutdown the current size of the window is saved as the configuration. People who don't re-size the window should not see any change until they mess with which tabs are where. When I think it through, overwriting the configuration probably needs to be a preference because there is bound to be someone who likes the resizing when tabs are added or removed from start up. Even with that there are probably some things people will complain about where the work around begins with "edit your settings file"...