As pointed out in the thread, it says the same thing for Python2 (though only if you run it bare for some reason, not with --version, and obviously only if you're invoking the system Python2, not something from e.g. Homebrew) so it seems to just be the message they use for anything that's deprecated and expected to vanish from macOS installations in the future. I bet the same message is used a bunch of other places.
I'd be kind of horrified if anyone's writing PHP on a mac that is not targeting the system's PHP specifically, but is using it. You want whatever version's gonna be on your deployment target, not what happens to ship with your OS installation. Included scripting languages are there so you can write scripts targeting the OS, not develop with them generally. You could, but it's not what most people are going to want.
People are really bringing up the pitchforks over nothing...
Pro: You don't have to download it, it is already there
Con: It is always going to be an old and outdated version, since Apple can't keep up with the open source developers, so you probably need to download it anyway, and then deal with the confusion of having both the old and new versions installed
They probably didn't foresee how it was going to work out in practice, in hindsight they probably wish they'd made a different decision. You learn from experience.
Also, Unix OS vendors have had a historical culture of bundling things. Back in the old days, before widespread availability of the Internet, it made sense to bundle as much with the OS as possible, since if it wasn't bundled it was hard to get. Even after the Internet became widely available, back in the dark ages of dial-up, downloads were so slow, it made sense to include as much as possible out of the box. It is a different world now. But keep in mind that Mac OS X Server 1.0 was released all the way back in 1999, and back then those times were still the reality for many people, and a recent memory for many more.
`WARNING: Python 2.7 is not recommended.
This version is included in macOS for compatibility with legacy software.
Future versions of macOS will not include Python 2.7.
Instead, it is recommended that you transition to using 'python3' from within Terminal.`
Similar message for Ruby, but without the "not recommended" part:
`WARNING: This version of ruby is included in macOS for compatibility with legacy software.
In future versions of macOS the ruby runtime will not be available by
default, and may require you to install an additional package.`