I agree that the magic bonuses don't make sense for a Redguard.
However in Oblivion arguably the most skilled mage in the game was Borissean (a Redguard), master spellmaker in the Arcane University. And Delmar (also a Redguard) is perhaps the only mage skilled enough to make a mage's staff.
And the mage you mention in the OP, Traven the Redguard, mostly complains about illusion and conjuration magic, not so much alteration and destruction. In fact Traven sells some low level alternation and destruction spells.
There was also Azani Blackheart, a very powerful Nightblade. Oh, let us not forget the few necromancers encountered in the game, also Chanel, Treyvond, etc.
But yes lore-wise, those bonus don't make much sense. Speech would have made more sense, and maybe light armor.
Coincidentally Redguards gained the mercantile skill in Oblivion, with the obvious loss of medium armor from Morrowind. With the shrinking of available skills from game to game this change actually made some sense.
So what was the reasoning behind the latest change? Perhaps we'll never know, but I'm not all that put off by it. With only six skills within each archetype it may have been just a balance adjustment or maybe BGS "nudging" players to dabble in the new magic system. Of all the races in Skyrim it is only the Altmer that are strictly set to any archetype (magic).
As Savlian and many others have pointed out, it's like any stereotype; there will be exceptions. Hell, Orcs now have a bonus in enchanting. Talk about moving up in the world...