It might be an option to fail early when you set the strategy to 'include', but only if we know that the copy spec is going to be used to copy to the file system.
As far as last-wins goes, I think we should make that a separate option. The idea is that a copy spec should give you the same result regardless of container, and right now 'include' gives you last-wins when copying to a directory and all when copying to an archive.
I think we were a bit eager with the warning, as you can only get rid of it using an incubating feature, and it would make sense to add filtering for identical files first. So, I reckon for 1.7 let's just get rid of the warning.