What you can do for now is to save your work once you have worked with it, and then reopen it in gimp to set and crop the file size you want.
Then reopen it in mypaint if you want to continue to work on your image =).
You can also start by creating a file of the format you want with a frame around it, then open it in my paint.
I think the developpers are working on being able to set this or not in mypaint, just be patient =).
Have a good day !