WR rod is longer then any yfz (atv) rod given equal stroke. So the rod to stroke angle is better, TDC is taller in the bore which = more compression. Which is exactly why the wr449cc motor is 12.5 compression and the 06+ yfz 449cc motor is 11.4. Same stroke distance, same bore, but being taller in the bore at TDC = more compression.
You will not notice any rev speed trail riding, so I wouldn't worry about that.
You may notice a WR crank vibrate more. Some feel it, others do not.
IF you want the 10cc gain of the WR or 06+ crank, IMO get which ever crank you can get a piston for and for the cheapest amount. Between the 2 cranks, wr and 06+ for trail riding IMO they are pretty close to being the same. If WR pistons are harder to get... 18mm wrist pin vs. 20mm for the yfz then stay with a yfz crank. Piston choices "may" be easier to come by.
Like I mentioned earlier, gearing will play a bigger roll in trail riding then crank mass. If you get real anal over it, you could go with a heavier flywheel from trail tech. I personally have never liked Trail tech's lighter weight fly wheels, as they crap out, so I never consider swapping out a proven fly wheel like a OEM Yamaha designed unit.