The announcement says to post here if you run into false positives.
Though for the last person who did so, it didn't seem like Let's Encrypt was going to be able to make exceptions so easily.
Just posting those links to give some context; I think we'd need to wait for someone from Let's Encrypt staff to post to get any sort of definitive answer.
As a workaround, if you need something more urgently, you might want to look into trying some other CAs if Let's Encrypt isn't going to be able to support you. There are several that are also free and support the same ACME protocol for automatic use. There are some comparison charts from the author of Certify the Web and from the author of Posh-ACME about possibilites you might want to explore.