Regression was introduced while attempting to fix case 1040726 (https://issuetracker.unity3d.com/issues/primary-screen-window-size-turns-to-native-when-using-more-than-one-display)

With this new fix, the initial state of the primary display will be based on the current FullscreenMode when multi-display is activated:

- If running in ExclusiveFullScreen or FullScreenWindow mode, the primary display will have a "fullscreen window" matching the native monitor resolution
- If running in Windowed mode, the primary display will have a "borderless window" matching the current width and height

To change the window size on the primary display, call Display.SetParams() *after* activating the primary display.
For example, to force 640x480 windows on both displays:

// Display.Activate() parameters are ignored for the primary display (index 0) so just pass in 0's
Display.displays[0].Activate(0, 0, 0);

// Activate the secondary display to use a 640x480 window
Display.displays[1].Activate(640, 480, 60);

// Force the primary display to also use a 640x480 window
Display.displays[0].SetParams(640, 480, 0, 0);