However, I get the feeling that this gives the magical traditions twice as many abilities as the non-magical traditions (thematic features only, no spells).
Sure, I can see that. I don't think that a spell list is worth much in itself - the MAG increase is the key thing here. Additional spell lists make you more versatile, but they don't make you more powerful. A spell list just unlocks access to stuff - it's saying "hey, now you can use your high MAG score with fire as well as plants", kinda like a soldier ability saying "hey, now you can use your high AGI score with a pistol as well as a rifle!"