I guess I should weigh in on this. Because, well, I am the GM that caused Blargney's initial concerns.
So, we have a rule at our table that basically amounts to "When using the Character Builder, we do not use anything from DRAGON magazine". While you can say that's unfair or whatever, I just figure it saves me from one major headache. And we've been pretty good with it - people have accidentally taken dragon feats, and then corrected the problem with a heads-up to me.
The big problem came when Blargney put his minotaur PC through the CB, and realized he lost Oversized. Since he was playing a fighter that was built towards offence over defence, it kind of hurt his bottom line. However, at this point, I was kind of thinking that oversized had been errata'd out of the MM, and felt that there was a good reason for it (also, that it made sense - the minotaur fighter does a lot more damage than the Dragonborn Paladin).
To compensate though, because the minotaur lost a big "power", I offered Blargney the Iron Armbands of Power, a previously "no" item - essentially, balancing things out a little bit. Which I thought was a fair trade.
When we realized that the new minotaur was from DRAGON, though, I Had to repeal that rule, because it'd be kind of lame for me as a GM to say "you can't use any of the good stuff from dragon, but anything that screws you guys over has to be adopted". So, I took back my initial ruling, and went from there.
Really, I have NO problem with PC races being different mechanically than non-PCs of the same the race. Because, really, the only person who will notice (most of the time) is the GM.