Browsers sometimes charge ahead. I woul them rather to do that with prefixes than without. I don't think that's in any way comparable to Microsoft's behavior.
Charging ahead with prefixes is sure better than without.
Doing that and encouraging web authors to create public-facing sites that depend on the prefixes to work correctly (which is what Apple has been doing) is no different from Microsoft's behavior around 2001, imo.
Well, Apple is doing all kinds of weird stuff and Apple is also not Webkit.
I think that 3D transforms in CSS are inevitable, there is consequently nothing wrong with browsers testing the waters. Implementation and standards always had an organic relationship, sometimes the standards are ahead and sometimes the implementations. I think that’s how it should work, I think that strengthens and accelerates the process. The standards frontier of the web will always be messy and I am honestly happy that standards bodies are finally willing to embrace that messiness.
Apple encouraging the use of CSS properties with prefixes, even if they are brand new and there are no implementations in other browsers or even plans is a different issue. Luckily nobody listens to Apple when looking for advice regarding web development ;-)
I personally think that you shouldn’t use 3D transforms at the moment for anything you intend to be used. Neat demos are ok.