Yes, it the base can deprotonate the hydroxy group ultimately bringing us back to the original carbonyl.
However, the same choice exists at the hemiacetal stage in acid. We can either protonate the OH group, leading to loss of water and ultimately acetal. Alternatively, we can protonate the OR group, lose the alchohol and return to the original carbonyl. In the end, both happen and we end up with some sort of equilibrium between carbonyl, hemiactal, and acetal.
Now, back to the hemiactal in base: Unless the activation energy for the the Sn2 displacement of the hydroxy group by the alkoxy group is especially high, we would expect to settle out at some sort of equilibrium between the three just like we do in acid.