No, you can't customize the size of the default canvas, yet.
I think something like this in the works for v4, but I might be utterly wrong.
But if you just want to paste something from the clipboard to a new image, use Edit > :PasteNewImage:Paste in to New Image instead of creating a new image and pasting the content in it.
Note that Paint.NET automagically knows the dimensions of the picture in the clipboard, and suggest them in the "New..." dialog, so you can just hit Return anyway.