Promise chain continues before inner promise is resolved

You've done nothing wrong here. This is jQuery's fault, as so often¹.

The problem is that jQuery is not Promises/A+ compatible (until v 3.0), and fails to adopt promises/thenable from other implementations than its own. So when your callbacks do return RSVP promises, jQuery just treats them as values to fulfill with, instead of waiting for them.
You could cast all of your promises to a jQuery deferred and it would work, but you really don't want that. To get the standard Promise behaviour (as offered by RSVP) to work, you will need to avoid jQuery's buggy then. This can easily be done:

RSVP.Promise.resolve($.getScript("/_layouts/15/SP.RequestExecutor.js"))
//   ^^^^^^^^^^^^^^^
    .then(patchRequestExecutor)
    .then(function(){
        sourceExecutor = new SP.RequestExecutor(sourceFullUrl);
        targetExecutor = new SP.RequestExecutor(targetList);
    })
    .then(getFileInformation)
    .then(getFileBinaryData)
    .then(copyFileAction)
    …