If you use unofficial overclocking mode without powerplay, whatever you set the core to, once youve hit apply, it stays like that in 2d and 3d. So you can have a 3d and 2d profile saved, or just use 3d mode to fix the throttle issue, then hit reset button once finished gaming.
They save power by dropping the core clock, they also let the fan spin slower so are less noisy as not as hot with lower clock, but performance takes a massive hit as in some cases a drop of 35% on the core clock is probably putting the card on par with a r9 280

If gaming at high resolution, ultra'd out, the core dropping this much causes fps to suffer and microstutter when its occurring.
Majority of people who buy an r9 290 arn't going to be worried about a few watts, or the fan spinning a little higher, especially on the aftermarket quieter coolers, so AMD should just lock the clocks under 3d.