How about because all those you list don't have user interface ties. Maybe because all those you list aren't heavily used by the majority where an outdated or exploit-prone version would matter. People who do use the examples you listed often install their own versions because the Apple versions are out of date.

Apple can't fix bugs in Flash.

To the extent that Apple depends on (say) Ruby, then they own the system ruby and have a responsibility to keep it up to date. So, for instance, when someone finds an Apache flaw, Apple has to bundle a security update for it, and may even have to alter ship dates to account for it.

To the extent that Apple can decide that it does not depend on, say, Flash, then it makes sense for them to not to ship it. If they ship it, they own it, they have to fix it. If they don't ship it, they don't own it, and the vendor has to fix it. Which, in Adobe's case, makes perfect sense; Adobe's security flaws should not be Apple's problem if they don't have to be.

Look at it the other way. Why should Apple ship software it can't take responsibility for? Does Silverlight come bundled on Snow Leopard?

Darwin is a decent UNIX-like operating system underpinning OS X. The inclusion of standard open source packages like the ones you mentioned increase the utility of the system for the extremely valuable minority of OS X users who happen to be programmers with barely any far-reaching implications for the vast majority who never touch them.