IMHO, if you are going to suppress it and reload, go with 300blk. Otherwise, x39 is the way to go. If you don't reload and/or have a free brass or other reloading hook-up, the price of 300blk ammo is about more than twice as much as x39. If you shoot a lot, they'll be a huge cost and time difference.
Sure there is a mag and bolt difference between the 223/556, but so what? It's not like you can fire both 2.23 and 300blk out of the same upper. They both are dedicated uppers, both of the bolts, if purchased from a quality company, will likely never need to be replaced, and if it does, replacements for both can be found online.
As far as mags are concerned, there are reliable x39 mags that fit the milspec AR lower now. Yes, they are a little more than AR mags; however, it'll be much, much cheaper in the long run when you compare that against the cost of shooting 300blk.
It all depends what's more important. For me, I do not reload nor do I plan on shooting suppressed. I can find mags and bolts for both calibers online. Even though x39 bolt and mag selection isn't anywhere near that of 2.23/5.56, those aren't components that will likely need replacing anytime in the near future or my lifetime. If I can afford to shoot that much ammo, I can afford a couple of back up bolts... While there's a lower selection of bolts and mags, there's a higher of a selection of ammo which is something that will need to be replaced often and, unlike 300blk, can generally be found for cheap anywhere ammo is sold..
