What a gorgeous rattie he was
I don't really know anything about rats and how they should be kept but sometimes I think we have to go with our gut instincts more than what the norm is. You clearly had a very special bond and understood his needs. It sounds to me like he was very happy and his cuddle at the end was him letting you know that he appreciated you for loving him letting him be himself.
I'm sorry for your loss, RIP Tolkien