I have a .300 WBY mag and love it! Have never owned a .300 WIN mag, but have shot a few and the recoil isn't too far apart. WBY will punch a little harder. I am not a Weatherby fanboy, or any other kind of fanboy for that matter, but I believe this is one of the best rounds out there, especially for long ranges. The only reason I believe it isn't as popular as some of the others is the ammo price. Most folks don't want to spend 2-4 bucks a shot. The average feller would rather take a more common, good performing caliber with cheaper ammo. Of course, a 1000 yard gun isn't an average gun, by any stretch of the imagination. And, in my opinion neither is the .300 WBY mag caliber. Worth all the consideration you would give it.

That being said, I do not at all think you would be making a grave mistake by going with the .300 WIN mag, but my preference would be the WBY. Have fun with your decision and soon to be rifle!