emacs のデフォルトのウィンドウサイズはオプション画面から
Environment -> Frames -> Initial Frame Alist と辿ると

----
    Alist of parameters for the initial X window frame. Hide Rest 
   You can set this in your init file; for example,
 
    (setq initial-frame-alist
          '((top . 1) (left . 1) (width . 80) (height . 55)))
 
   Parameters specified here supersede the values given in
   `default-frame-alist'.
 
   If the value calls for a frame without a minibuffer, and you have
   not created a minibuffer frame on your own, a minibuffer frame is
   created according to `minibuffer-frame-alist'.
 
   You can specify geometry-related options for just the initial
   frame by setting this variable in your init file; however, they
   won't take effect until Emacs reads your init file, which happens
   after creating the initial frame.  If you want the initial frame
   to have the proper geometry as soon as it appears, you need to
   use this three-step process:
   * Specify X resources to give the geometry you want.
   * Set `default-frame-alist' to override these options so that they
     don't affect subsequent frames.
   * Set `initial-frame-alist' in a way that matches the X resources,
     to override what you put in `default-frame-alist'.
----


つまり手動で.emacsを書き換えないといかん。
フォーマットを統一させたいからなるべく設定メニューから.emacsを
設定できるといいんだけど、どうしてもこういう方法でしか
変更できないものもあるってことか。