Apple can fix this as @pfg said. It's just a matter of them choosing to do so. Why don't we all open tickets with them specifically requesting that they add LE support?
I found this email for opening tickets for podcast-related stuff: PodcastSupport@apple.com. If we all message them, creating a bunch of tickets, hopefully it'll put some pressure on to update their trust store and let us use LE for podcasts.
EDIT: if you want to make it really easy, here's what I wrote so you can copy/paste:
Please update your SSL trust store to include Let's Encrypt SSL certificates! iOS, OSX, and macOS all trust Let's Encrypt sites, so please add it to iTunes as well. It's extremely frustrating that we can't submit podcast feeds that are SSL encrypted using Let's Encrypt. Let's Encrypt is backed by Google, Mozilla, Automattic, and others. Please fix this asap.