1. The fox still has chakra left over because it needs some to maintain its existence and would die if it had all of its chakra taken therefore taking the chakra with it.
2. Naruto cant summon all the chakra from the fox because of the equivalent exchange law mentioned in the manga, it was stated that for every unit of the foxes chakra Naruto took the fox would steal some of Naruto's chakra in exchange. This is not a 1:1 ratio however due to the difference in size of the chakra's of the two beings. The amount of fox chakra naruto can utilise is solely dependent on the amount of chakra he has himself. it remains to be seen if nature chakra affects this balance as Naruto is yet to use sage mode and fox chakra mode at the same time.
3. Naruto is yet to fully control the fox's chakra and also has nothing near the relationship bee and the eight tails have which allows them to support each other in the amount of chakra each takes. instead of like the fox which would gladly take all naruto's chakra and take him over if it could this should change in the future.