Okay I did some research, too. The <extra> element seems to be an element within Collada files that stores "additional user-defined or application-specific information". My guess would therefore be, that the fact that it's missing is not important, since it's optional.
I also found this:
<matrix> element represents an accumulation of transformations;
<rotate> element represents a rotation about an axis;
So the matrix stores all transformations (translation, rotation, scale) of the joint and the rotate only stores the rotation, I guess? There are more than 9 numbers in the matrix element, tho...
Here's the source btw, in case someone really wants to dig into this stuff.