My approach is to avoid code generation. Bad formatting is the least of your worries.
It's not too hard to build a GUI with straight Swing if you get to know a few layouts (border and flow at a minimum), and you can also create routines to automatically generate your GUI based on your data or metadata--a nice trick that a GUI builder cannot even start to do (but if you're using a GUI builder, you'll probably never even try to make it data driven).
Personally I'd like to see more builders that generate a "Class" file instead of a "Java" file--something with nothing but controls laid out in a reasonable manner, allowing you to access the controls remotely either through a getter or something. (Heck, since it's such a specific use case, I wouldn't even have a problem making the members public..).
Objective-C does something like this, it's only the second builder I've seen that doesn't try to use code generation (the first was a private one we built for a product I worked on a long time ago that never got very far)