aa11 if you can find and install some ACME client other than certbot that is capable of using the alternate chain then you're free to try to use it to issue a a certificate manually. I can't think of any reason why it would not be possible.
The easier option would be to purchase a certificate from some other SSL provider.
FWIW we've had no other reports of problems related to this issue and I don't believe it warrants much concern.