When the Jahmiyyah and Mu'tazilah began to deny Allaah's Attributes they could not openly say, "Allaah is not above the Throne" because their falsehood would have become known to all people with sound fitrah and they would have been such rejection that they would not have survived it. So they only hinted and alluded to it at the beginning but the Salaf were wise to these Jahmites and Mu'tazilites - as early as the time of Ayyub as-Sakhtiyaani (d. 131H).
And the reason why the Jahmites and Mu'tazilah (and after them the later Ash'ariyyah) had to deny Allaah is above the Throne was because they had used an intellectual proof called "Hudooth ul-Ajsaam" against the Atheists in order to prove the universe is created - and the underlying concepts for this proof were based upon the metaphysics of the Greek Philosophers and particularly Aristotle. Their proof lay in claiming that the presence of qualities (sifaat) incidental attributes (a'raad) and events (hawaadith) in what we see around us of the bodies that make up the universe is a proof that they came about, occurred after having not occurred and therefore are created , and following on from this that the universe must have a creator. However, when the Atheists said to them, "Describe your Lord to us", they could not describe Him with what is found in the Book and the Sunnah, because it would amount to Allaah being described with incidental attributes (a'raad). And because they considered their proof to be decisive (over what is found in the Book and the Sunnah), they rejected what is in the Book and the Sunnah to varying degrees - the Jahmites negating it all and being the Imaams of Ta'teel. And the others, the Mu'tazilah, Kullaabiyyah, Ash'ariyyah and Maturidiyyah simply inherited something of their ta'teel. And the arguments of these factions and refutations are only in relation to what can and cannot be denied for Allaah, or affirmed for Allaah, in light of this false and corrupt proof that they are all united upon.
So the early Jahmites and the Mu'tazilah, they wanted to deny Allaah is above the Throne, as that is the greatest obstacle and invalidation of their proof, but they had to only hint towards it at the beginning. And thus we find the statements of the Salaf found below.