Nice guys finish last, Tomas. It's a beta so I say do whatever you have to do to make the product as good as it can be when it is released. It would be a shame to see a v1 product burdened with the cross of backwards compatibility with a beta.
Perhaps if I can offer a suggestion regarding re-creating extensively configured web parts... Maybe you can provide an option to configure the web part with some external XML files, or at least XML that could be entered into the web part properties pane. That would make it easier for users in the future to move their customizations between staging and production environments and make it easier to deal with changes to the interface.
Kinda like how PowerGadgets can be customized with .pgt files.