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