I believe if you upgrade to Elite on a server with a Rank Upgrade paper, you will only be Elite on the server(s) you used it on. You'll otherwise still be MVP+ everywhere else. So, certain global permissions that store bought elites have (such as the ones you mentioned like /shout, /gkit elite, and free seasonal crate keys) wouldn't apply because these are perks that can be used by store bought elites globally.
Perhaps a way could be implemented for rank upgrade Elites to only be able to claim their elite items or only be able to shout from one server? But at the same time, you didn't have to pay real money or full price for Elite if you used a rank upgrade paper. This is fine, I personally wouldn't mind if you guys got perks on the server you used the paper on. But also, rank upgrades are server based and aren't meant to work globally necessarily.