My understanding was that if the full resolution original was downloaded to your Mac, that higher res version is no longer stored in iCloud. But that's just my interpretation of the support articles and could be completely wrong.
I don't think that can be right. How about the case where you have two Macs and both are set to download full resolution?
Photos in iCloud storage is 540GB but the my Mac Photos Library is 640GB
You should be comparing iCloud storage with just the originals folder inside the Mac's Photos library.
Mine with Download Originals:
Photos and iCloud both report the same number of photos (2687) and videos (63) - total 2750. Plus 30 recently deleted. That is good!
iCloud storage reports as 19.64 GB. Photos Library (originals folder only) is 21.21 GB. Whole library is 22.93 GB. So compared with iCloud, originals folder is about 8% bigger and the whole library another 8 % bigger.
Whilst both report same number of images/videos, the originals folder (within Photos library) has 2827 photos and 185 videos - total 3012.
Confused? Maybe.
Some possible explanations/thoughts:
1) Partial explanation of size difference: Don't compare iCloud size with the whole Photos Library on the Mac. Only compare with originals folder on the Mac. But that still leaves a significant difference.
2) Possible explanation of different counts: The difference in count of images/videos and count of files could arise from photos have multiple components. They may have both short video and image - reported as one image in Photos and iCloud, but stored as two files on the Mac. Also some of my photos have both JPEG and RAW files.
3) Regarding total size, I conclude that Apple is not counting everything in iCloud.
More importantly, I’m concerned that iCloud Photos doesn’t have all my Mac photos and not sure there’s any way for me to check.
1) If the counts are same, it is most likely ok.
2) Do a test by downloading a few objects from iCloud (via web interface) and compare with objects in the Photos Library.
3) Make sure you have a good backup of the Photos library.