Very interesting! I have been thinking about something similar, but rather than learning from examples, it would have a generic "misaligned" cost function that would penalise lines which have similar content but in different columns, and minimise this by hillclimbing or similar.
The difficulty is tying it to a particular language's parser and whitespace rules.
Interesting, though it is a framework very similar to previous work using Box combinations. Here, we don't require any work from a language expert. We simply sniff your project, and then make new files look like those. Handling a new language requires no coding.
CodeBuff is also learning from examples. Check out the paper at the SLE conf; it has all the nitty gritty details how it learns the whitespace rules from the example files.
The difficulty is tying it to a particular language's parser and whitespace rules.