To be clear, this just means that PHP has libsodium as an official language extension. Most modern languages have better package management than PHP and make pulling it in as a library trivial.
This has nothing to do with homomorphic encryption, unless I'm missing something.
composer require some/library
That's PHP's package management. What's so non-trivial about that?
And, as a bonus feature, composer install won't automatically update your lock file!!