You're absolutely right to be cautious when things seem too easy. But, here is some reason why option 2 and 3 is bad options

Option 1 (some server like Apache/FastCGI) :

• "Boring and obvious" — yes. But there's a reason it's a standard.
• Mature and well-supported architecture.
• Easy debugging, monitoring, logging.

Option 2 (run builded in php server php -S localhost:8000) :

• "Easier" – true. But there are gotchas.

• Not production-ready: PHP’s built-in server is single-threaded and not intended for production use.

• No HTTPS support, no access logging, no protection layers like mod_security.

• It may hang or drop requests under load (even low load with SSR + multiple API hits).

Option 3 (use cli command form JS on server side like php index.php --someController='MyController') :

• "Must be faster?" Maybe. But... here's the devil in the details.

• You lose all the benefits of an HTTP server, No persistent processes, no connection pooling, no caching.

• Harder to scale later (parallel CLI processes can spike memory/CPU).

• Error handling is painful – think stderr, exit codes, etc.

That is my opinion about it, let's share about your thought.