The goals of FAH are first and foremost maximizing good science. Points are important, too, getting more points for exactly the same scientific throughput is much less important than actually improving that throughput. Most of the higher priority changes that PantherX refers to actually improve the scientific throughput for everyone.
Passkeys are NOT required, though they are recommended. All that information about passkeys is readily available in the FAQs and in the how-toos (and here on the forum) but when people choose not to read the FAQ and time has to be spent encumbering new software with popups reminding them of things that they can learn with a (very) little reading it seems like a poor use of expensive development resources. Can't Stanford assume that Donors who happen to be interested in points take a certain amount of responsibility, themselves?
OK .... I'll get off my soapbox now.

None of the third party utilities actually "flag optimal usage of clients." They have no ability to know whether your passkey is qualified or not. The have to
assume either that you'll get a bonus or that you won't get a bonus. You were the one that noticed the discrepancy, not the 3rd party software ... and as a result of noticing that discrepancy, you were the one who asked the right questions ... not some software.