Bit of a novel for you in case you were curious, but in TL;DR form, it's worked.
There was no error, it was just not generating the encrypted credentials. I should say there was a 404 error when running the AWS CLI commands, due to the bucket object not existing - though the bucket existed, so I assume the problem popped up somewhere between vault initializing, encrypting & then sending the keys to S3.
I was unable to properly diagnose it without any explicit error output, but after poking around I noticed a lot of the resources such as the EC2 instances, load balancers, etc - were still in a "Terminating" state while I was rerunning the terraform destroy/apply commands. I decided to wait a bit and try again.. Also learned that a full destroy isn't necessary in this type of scenario which is nice to know :)
I cloned the repo again today and started from scratch, and it's worked now with the aws_s3_bucket_server_side_encryption_configuration resource! The S3 bucket properties now list default encryption as enabled and Server-side-encryption as Amazon S3-managed keys (SSE).
Conor