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From the title of your question am I right that the source AMI that you're using is FreeBSD? The knowledge doc you've linked to describes how to create an Amazon Linux (not FreeBSD) AMI to deploy with EKS. This would make sense as I wouldn't expect amazon-linux-extras to be available on FreeBSD.
If you start off with an Amazon Linux AMI can you ovcecome this obstacle?
PS one more thing - use Amazon Linux 2 (not 2023) as this one contains amazon-linux extras https://aws.amazon.com/linux/amazon-linux-2023/faqs/
Q: Does AL2023 have Amazon-Linux-Extras like AL2?
A: No, AL2023 does not have extras.
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Yes, if i will be using Amazon linux AMI with the script from the repo i have linked in the question everything works well, as it does have this package, but yeah, it seems that the script is not Freebsd compatible, even thought it is said "build you own custom eks optimized AMI"... sad.