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Ok - I found the answer which consists of editing the /etc/amazon/ssm/amazon-ssm-agent.json file. This file has various sections where you can specify the endpoint and from what I can work out...
Mds Endpoint = ec2messages VPC endpoint
Ssm Endpoint = ssm VPC endpoint
Mgs Endpoint = ssmmessages VPC endpoint
So you just specify the route53 public VPC endpoint hostnames in this file and restart the agent.
This appears to be entirely undocumented but I have had confirmation that customising the agent in this way is a supported configuration.
answered 4 years ago
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