Comparison to TurboLinks
Really interesting project!
It seems really similar to the TurboLinks project (https://github.com/turbolinks/turbolinks)
I think your comparison to Ajaxify holds true "What makes React-Magic different is that it only updates the DOM nodes that have changed, whereas Ajaxify and similar solutions just blow away the whole document.body on every page load" except TurboLinks also caches previous pages.
One of the big problems with using TurboLinks is that scripts that rely on on document ready hooks are not executed as expected. I would assume this would be the same case.
Also TurboLinks has a directive for marking a DOM element as "permanent" which means its preserved across page loads. This is obviously the default in react magic. I wonder if there is a case for a similar markup in react magic but to do the opposite - force tear down of a component so that state can be reset.