I have a problem with Arabic. I put a top and _top anchor in father-ar and made fathatan-ar automatically. However, the resulting double components do not respect the anchor position; they kind of do, but they are somehow shifted to the top right. It also happens at the bottom double marks. Is this an expected behaviour? 
This is not intentional. Can you send me the file?
Sent
The problem are the metrics keys. If you remove them, it works as expected.
Thanks, but why do the metric keys matter?
The metrics keys were wrongly applied to all aligned components. I fixed that.
And I fixed that you finally can automatically align marks when they are the first component.