He is probably just syndicating this to medium with the new api's introduced.
I don't think they would have done that if there was a knowing SEO downside. It would hurt everyone.
<link rel="canonical" href="https://medium.com/engineering-at-ifttt/data-infrastructure-at-ifttt-35414841f9b5">
It would be relatively easy for Medium to appropriately set that tag -- I mean, if "original URL" is captured somewhere in the API, or in the Medium post-create-admin interface (I don't know, I haven't logged into my own Medium for awhile)...that would explicitly resolve the ambiguity, though at an obvious cost to their own SEO.