Besides cleanliness which is more a preference I agree, separating config, data, and cache makes it easy to know what can/should be backed up, what can be synced across machines, etc.
As I said in a different comment here, I have 94 files and folders in my home, 84 of which are hidden, approximately zero of which actually needed to be hidden.
If anything, it's the reason this is such a common issue, the dot lets everyone shit files out all over the place but oh it's hidden so no big deal.