From the list above permissions to the shop, usergroup promotion and your built in custom items have an effect.I see.
What about if you add an item that changes any of the built-in XenForo permissions as opposed to Shop ones?
(Change Username Style) 4 purchase 4 active
(User Title Change) 3 purchase 3 active
(steal chance) 4 purcase 4 active
(steal more) 4 purcase 4 active
(Immunity) 1 purchase 1 active
(sticky thread) 1 purchase 1 active
Personally I think every item will have an effect, some more than others as you can see above.
I did a fresh install on the shop and with no items it has no effect on the time. My forum only has a few hundred members, imagine it had thousands like yours, I bet it would be much worse.