Just curious to what the logic was behind that, or why it ended up like that, any input would be appreciated.
The problem is that you're assuming the division of Germany from 1948 was intentional and planned from the start.
The division into zones of occupation was always intended to be temporary until such a time where a formal peace treaty with a German government could be signed.["a peace settlement for Germany to be accepted by the Government of Germany when a government adequate for the purpose is established." Potsdam Agreeement, I,3,(i)].
Berlin as the capital was divided in the same way that Germany as a whole was [London Protocol, 1944], likely because of its importance and to ensure that no one power held the capital alone therefore giving it more 'importance' than another. Berlin wasn't 'knowingly' created as an enclave in an East German state that was never intended to exist.
The division into occupation zones was an administrative measure, and it was done with the intention that at some point in the future, these would be united under a domestic German administration. This new German government could then sign a formal peace treaty and formally end the occupation.
However, given the breakdown in Allied-Soviet relations from 1946, this became increasingly unlikely to happen as the two sides simply could not agree on almost anything, let alone something as important as the formation of a new national German government and peace treaty. By 1949, two German governments had emerged, stranding the jointly-occupied Berlin in the GDR - but this was a consequence of unfolding events, not intended from the beginning.