Thanks to @danminneyatsaf for answering my previous question about the SQS Trigger in Automation and certificate failures.
I was able to solve because SQS has a Queue URL in the parameters for the trigger and register the SQS certificate as a trusted certificate on FME Server.
With S3 when I try to connect I get the following error again. The "Bucket to Watch" is the bucket name. I've tried going to the bucket url and using the certificate from there and still have the problem.
Any ideas which address the S3 trigger is going to?