Packages that you will install are Ford’s, CyanLabs just created a tool to facilitate the access to them lets say. You do not need to JB anything, since everything is done according to Ford’s methods.
Well, technically that would void the warranty. To what extent, will depend on the dealer. But if the find out the APIM is not stock, of course it should not void the engine or gearbox’s warranty.
Mostly, they just do not care nor loose time in finding out what really happened to the APIM. And, if you are paranoid, you can always downgrade to 3.3 which has the same look and feel as 3.0.
If your unit is 100% stock, you should be fine.
Only “issues” are with aftermarket modifications or configuration modification performed by users prior the upgrade. The upgrade may set those settings back to original values.
Also, you would end the process by performing a Master Reset, so you will have to reconfigure BlueTooth and all customization.