Thank you both for providing a solution.
I have found an even easier way to work around this issue. (Certificate creation works, Please revoke and reissue each certificate to make sure renewal is also using ACMEv02)
The latest Let's Encrypt i-MSCP plugin is using certbot 0.26.1 which is already capable of using ACMEv2. But it is not used by default.
You can change that by uncommenting line 796 in /var/www/imscp/gui/plugins/LetsEncrypt/backend/LetsEncrypt.pm so it looks like this:
Please keep in mind, that this files gets overwritten, when reinstalling or updating the Let's Encrypt Plugin.