Extended classes should be able to reach the regular max level if they have a class advancement that allows them to go beyond 99 like Rebellion, Kagaru/Oburu, and SN. However, if they don't have a class advancement designed to go over 99, I'd rather see them wait until they've created that instead of arbitrarily letting them go over 99 just because.
Which is why I'm also personally against letting 2nd class/trans 2nd class go over 99. With the way the game is designed to flow currently, you get to 99, change classes, then move on to 100+. It doesn't make any sense to me just to let 2nd class/trans 2nd class to just arbitrarily go past 99 without advancing into something more. If you do that you're just getting slightly stronger but no new skills which will make it harder to go against the higher monsters (yes I'm aware there are a few exception skills like acid bomb and Gfis, but for the most part 2nd/trans skills aren't as effective in the high level content).
Ideally, they should have given all the expanded classes new 100+ classes when renewal first hit instead of incrementally adding them in later leaving them gimped. But, as usual the devs were too lazy and now we're stuck with some people not being able to properly take part in the newer, high level content.