I read somewhere that hidden brackets actually make the shelf feel more like part of the wall, which looks nicer but is a pain if you ever need to tweak the height. Your flip to the outside is honestly what most people do when the holes don't line up, so you're not alone there. Visible brackets can look kind of industrial if you style around them, just depends on the room I guess.

Man, the wind rattle is what gets me every time. With zip ties, even the ones with a screw hole built into the head, you can never get them snug enough because the tie itself has to wrap around the cable and the mount. How much slack are you leaving between clips on those long runs where the wind hit it? I keep mine about 18 inches apart on the straight stuff, tighter on corners, and I'm wondering if that's why I don't get the same rattle issue.