I think the situation with Primal is a bit different - I think they don't count all nested replies and also they don't count reactions other than the default "like" (people on other clients react with different emojis).

But yeah, there are definitely differences across clients and relays in what you see.

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Ah yes, if you manually un-nest all the way the disparity is much less. Though if you do manually un-nest it does appear that, for popular enough posts, there's often some disparity, be it spam filtering, not indexing, or other.