cgmap.com is a common source, but they aren't the be-all/end-all bible. Geography can be an inexact science, especially in the sub-1% range that most of your examples illustrate. They provide you their data up front, so you know what you're getting. If you don't like the deviation from another source, you can always try another airline.

Hasn't the "actual flight miles" vs. route planned miles credit been addressed - making photographs of actual flight mile calculations a moot point? It's at least covered in the T&C's of the program, so you'd need to sue to get it changed.