You might want to be more specific about the meaning of "between" here. It's not a cryptographic MITM attack, and if it ever facilitated someone else in performing one, that should be detectable.

https://en.wikipedia.org/wiki/Certificate_Transparency

(It's also true that the level of active monitoring of CT logs has never gotten very high.)

It's not like Let's Encrypt is the only game in town, Actalis in Italy provides free ACME certs too if you'd prefer to keep things in Europe.

They are definitively not the most shady organization in the CA/Browser Forum.