Jesse, I hear you. When I lived in Santa Fe, NM for several years I was still in boot mode. On the other hand in my experience, if you are in true "sand pouring in" conditions boots might not keep it out entirely either. With the trail runners I can stand on one leg without taking off my pack, take off the shoe, empty it out, and put it back on in a matter of seconds. In boots you may just wait since it is often a big to-do to get them on and off. There is a bit of an analogy here with the water/Gortex issues. If you are in a place where there is soft sand for extended periods then, like water, the boots are nice right up until they get sand in them too, and then they are worse.
Full on boots to keep sand out might be what my dad would have called "five lbs of solution for a 1 lb problem". I guess in this case that's not even a metaphor. The solution that a lot of us use is not to use trail runners with super permeable uppers in those conditions, and to add a micro-gaiter like dirty girls. This covers the top of the shoe and seals off the ankle hole reasonably well. This works pretty well for cumulative sand and grit gradually seeping in.
In conditions that are in the extreme for sand – for example trekking up a 600 foot dune in the Kelso Dunes in the Mojave, I would still want runners since your feet are going to be sinking a lot into the sand, and occasionally even up to the calf, so dumping your shoes or boots multiple times is inevitable. I hate sand in my shoes, and pebbles even more, but only in boots were these ever major issues for me, and now I get it out of there right away.

