Though the latest info (which is awhile ago) is that you can go to 3rd classes from both non-trans and trans 99, you do miss out all the trans skills and the extra stats if you go directly to 3-1 and 3-2 classes.
Mind you that gravity is totally focusing on the Renewal and 3-1 classes have been delayed for over half a year (for good reason). The info is highly subjected to be changed.