Server.app and importing a Let's Encrypt Certificate
Private keys in the keychain have an Access Control List (ACL) attached to them. You can edit this list using the Keychain Access application. 


Open Keychain Access and select the System Keychain
Select Keys from the Category picker in the sidebar
Find and select the Let's Encrypt private key
Hit cmd-i (or double click) to open the viewer
Select the Access Control tab
You may have to authenticate
Click the "Allow all applications to access this item" radio button
Click the "Save Changes" button.


Then restart Server.app and try setting up the Services again.