All those points are true - though I'd argue this is stretching the "one app per VM" thing -, but I guess this is just the usual case of understanding your situation and realizing there's no one size fits all.
My take on this question is rather that there shouldn't be any dogma around this, such as disabling mitigations should not be considered absolutely, 100% harmful and never, ever, ever disabled.
In the context of the OP, where the application is running on AWS, backups, email, etc are all likely to be handled either externally (say EBS snapshots) in which case there's no issue, or via "trusting the machine", so getting credentials via the instance role which every process on the VM can do, so no need for privilege escalation.
So I guess if you trust EC2 or Task roles or similar (not familiar with EKS) to access sensitive data and only run a "single" application, there's likely little to no reason to use the mitigations.
But, yeah, if you're running an application with multiple components, each in their own processes and don't use instance roles for sensitive access, maybe leave them on. Also, maybe, this means you're not running a single app per vm?