@nebulon @scooke

I tried just using No-op DNS with the settings described in my initial post.

I now use my.mysubdomain.duckdns.org to get to the Cloudron dashboard.
pixelfed.mysubdomain.duckdns.org to reach my pixelfed instance.

Let's Encrypt worked and I do't get any error regarding SSL Certs from the browser, meaning https works.

However, I don't think that this step was actually necessary:

On cloud.linode.com I have used the "Domains" tab on the left to add my duckdns.org domain and I can see A/AAAA Records for both *.mysubdomain.duckdns.org. and mysubdomain.duckdns.org

NOTE: I realize that it was confusing to write my.duckdns.org as example URL, as cloudron is using my as subdomain for the panel.
I can't edit the original post any more, but if some day someone runs into the same issue and reads this post, be aware of it.