Yep.
The Luma's clock setting is set in a higher place in the chain of command in the 3DS, so it's permanent and you don't need to do it in NTR.
Note that this will obviously take more battery and reduce the autonomy.
If you play games that don't have slowdown or high loading time, you can set it to normal in Luma and only activate the clock speed in a particular game with NTR.
Note, that doing it with NTR only (so Luma's clock set to default), will reset the clock speed when you exit a game so you'll need to enable it again in the next game.