My solution was to create a saved file "My Scratch Pad.scpt", and configure the window it is in as I want it to be. This also has the advantage of saving my last "scratching".
For details, see:
I also have a couple of Keyboard Maestro Macros that will auto-configure the window layout when SD is launched, and to ensure new files opened in SD are opened in the main window (not the Scratch Pad).
If you, or anyone, is interested in these KM Macros, please let me know and I'll post. They are still in the final beta stage, but as soon as I have time-tested them for a bit, I'll publish on the KM forum, and here.