Thanks a lot for your quick answer. Unfortunately it doesn't help me too much.
The domain is correctly accessible on IPv4 and the validation process should automatically fallback in case of network unreachable - this is not a problem of a badly configured web server. There is an issue open on github, but it doesn't have yet any resolution.
I understand that giving more options when issuing certificates may be considered as a potential security issue, but in the end, choosing one protocol against the other is a question of taste. When IPv6 can still be considered in infancy, the validation code should be smart enough and show a certain level of tolerance.
In my opinion, after reading a lot of questions around this aspect, since something that worked perfectly stopped to work, preferring IPv6 against IPv4 is bringing more trouble for no obvious advantage.