I'm not sure the top level window has any properties anywhere.
I'm not too versed in wxSmith's internals, so I might miss something.
Preserving compatibility would be troublesome, unfortunately, you're correct.
Probably we'll have to use something like "// InitializeNoLayout(myClass)" and this would work for new code only or if the user manually changes from "//* Initialize(myClass)" to "//* IntializeNoLayout(myClass)"
This way it might not require adding "// InitializeLayout(myClass)".
Also I'm not really sure which is better to do.
Someone using wxSmith regularly should do some experimentation with both and tell us the results.

Other ideas are welcome of course and mostly patches, the probability for me finding time to work on this is close to 0!
But I can find time to review and apply patches.