I wouldn't worry about it too much. Three season tents rarely keep the wind out. And if it's really that windy, it'll be flapping so hard that you will have trouble sleeping anyways. If you're wanting something that doesn't let wind blow across you, you'll have to carry something that is completely enclosed. Tarptents aren't good for this.
The Moment is a good tent for the CT. There isn't anything unique about that place in comparison to other alpine areas when it comes to gear choices. I carried my Moment on the CDT last year. Your additions of extra stake points will make the tent much stronger, I've though about the same mod, but only in two spots. I'd encourage you to not dig holes, even small ones, at your campsite. LNT,'ya know? I also wouldn't bother with replacing the mesh with silnylon. You'll be getting wet from condensation on the walls of this tent (which will be shaking off on you if it's rainy and windy), not from water coming through the mesh.
I haven't hiked in the Colorado Rockies in July. I bet that it *could* be windy, if an "event" happens, but that it's not habitually very windy.
Have a great trip!