Site visits are not the same thing as advert impressions. Although they should share similar trends.
I’m not super familiar with Cloudflare but I can’t really say much about their inner workings. But I know of people who use CF and AdRotate without issues.
You can of-course count your stats in Google Analytics if you prefer, then both counting mechanics are the same and should line up more. This will also avoid any caching issues with stats.
As for Geo Targeting, CF forwards the original IP (of-course) and AdRotate Pro can detect that if CF follows the rules. Most VPN, Proxies and stuff like that are transparent for AdRotate Pro.