2) "Allowed" yes, disregarding the sanctions/embargo in place these last 60 years.
3) My geography knowledge is a bit spotty, but isn't Kaliningrad part of the Russian Federation (even if an exclave, between Lithuania & Poland)? Also I don't know if indeed there are nuclear weapons in Kaliningrad.
I am not arguing that NATO is worse, my point is that NATO is the West's/USA's tool and regardless of whether you see it as an instrument for justice/good, historically it very much has been against Russia's interests and arguably still is. You may consider NATO a force for good and Putin/Russia evil, thus giving legitimacy to NATO's existence & operations, that does not mean that Putin/Russia perceiving NATO as a threat "makes no sense".