Rather than utilizing the IP addresses mapped to instances in the hosts file you could instead create DNS records for the instances and refer to them for the application if possible. You can create a private Route53 zone in a VPC, add A records pointing to the instances via CloudFormation.
If it absolutely isn't possible via DNS records then you could do it via storing the hostname & IP in parameter store and then fetching it sometime after instance creation to add the host file entries.
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