I think Let's Encrypt's behavior is correct, and I don't think anyone inside Let's Encrypt or CA/B Forum would like to inflict "pain [...] on host and network operators" beyond the current practice. Let's Encrypt's current behavior could be described as cooperating with IPv6 adoption rather than compelling IPv6 adoption, which seems like a reasonable place for a certificate authority to be.
There are cases where Let's Encrypt has made choices that potentially slightly reduce compatibility in order to encourage what it considers technically correct behavior. The first one that comes to mind is
https://community.letsencrypt.org/t/adding-random-entries-to...
but I know there are others. On the other hand, all of those decisions can be justified in terms of improving the correctness of PKI software (like not hard-coding things that should not be hard-coded). I can't think of any example that's like "we wish this other technical thing would happen outside of the PKI, so we'll try to force it along", and I don't foresee the broader community getting comfortable with that.
There was a comment below that in the LE forums instead of asking people to fix their AAAA records, they ask them to remove it. That's exactly the behavior you don't want to reward, so you must cause pain.