Once you install AWS CLI, PowerShell continues to support all of the native PowerShell cmdlets, but it also supports AWS cmdlets. The way you can differentiate between the two is that all AWS-related ...

Unlike Amazon's web interface, AWS does not automatically update command-line tools such as the AWS Tools for PowerShell.

You can still automate Let's Encrypt even if your system requires a DNS challenge. Using these PowerShell scripts and Amazon Web Services' DNS service Route 53 will do the trick.