Everything doesn't index folder sizes, instead we ask it for the contents of the folder via a search filter and add the returned sizes up. Not as efficient as it could be but still a lot quicker than recursively reading the directory.
So if some files are omitted from the index and not returned by Everything then the folder size would probably be incorrect. Honestly I didn't know Everything had that ability so we didn't consider it might be an issue.
Give it a try and see if that is indeed what happens, and if so we'll have to see if there's anything we can do about it (probably it would just mean disabling the folder size calculation if we can identify that files have been omitted).