After playing the game three times, I'm pretty sure I can distinguish a Mastery bonus.
Yes, I'm fully Light-Sided, I got all the sparkles behind my character on the status screen and I have the stat bonuses. (+3 WIS for being a counsular & +3 CON for being a Watchman, IIRC.)
I can still gain a lot of levels, I still have to do Narshadaa, Korriban & Dxun/Onderon.
The point is: in other play-throughs, the crystal gave me the appropriate Light-Sided bonuses, which scaled with level. The crystal glowed "very brightly". Now I get different bonuses, which also scale with level. The crystal "glows faintly". Yes both times, I was just as much Light-sided.
BTW, bad points for Obsidian again for scrapping an entire planet and not rebalancing the things dependant up it.