Apple and Third-party frameworks
Even the blog acknowledges that there are problems, noting that it doesn’t integrate with the system keychain, but that these are “minor issues”.
Since Firefox doesn’t use the keychain passwords in Firefox are not subject to my keychain policy. I don’t know if the passwords are secure when I lock my machine, I can’t delete them using the administration tools, and they can’t be shared with other apps if I allow. This is a major issue, especially on a mobile device.
The important thing is the user would never notice that.
Firefox also doesn’t obey the system proxy settings. Granted, that’s useful for me, but imagine a corporate situation where there’s a company proxy. Start Firefox and it’ll ignore all system settings.
Then there’s the preferences dialog, which just throws the entire HIG out of the window.
While all this may be acceptable to many user, especially “power users”, this is not the experience Apple wants for the devices.
Games, of course, are a special case where the UI is almost entirely custom, but if developers get too “creative” it’s detrimental for all.