I'm pretty sure my one airline-credit stay (for NWA Pile on the Miles which requires activities with different partners) recently did increment my tier count, but it didn't show up anywhere else on the Choice site.
I know that in previous years I've gotten to Diamond only because miles-earning nights were counted. I had to call Choice to get that count (this was before their tier counter online), because there was no other way to verify if I had enough nights.
With all the bonuses this year, though, I'm about to get to Diamond requal soon anyway, so to me personally this year it doesn't matter in the long run whether my miles-earning nights counted.