CSS3 is not yet standardised, so you should not be thinking about acid3. some of the tests in acid3 were pulled and will not be in the final standard, so Mozilla are not doing them.
Safari (Webkit) runs some of the CSS3 tests in quirks mode, which is in none standard mode, it also doesn't animate, so not a true 100% score.
Mozilla's product cycle for Gecko came to an end when acid3 was produced, making them behind. Webkit's cycle came many months before, meaning they could complete their goal of getting a 100% score (but not correctly).
The DOM with Gecko is very standard compliant, unlike some parts of Webkit.