As asked in the title, can a Universe which is deterministic at its fundamental level still allow free will?
Personally, I think indeterminism is necessary (but not sufficient) to the existence of true free will. If the universe is deterministic, anything we call "free will" would be a superficial type of one. If everything is determined, no one is choosing anything, despite the impression we may have of doing so.
I think Koeng is dead on and summarizes succinctly the live options available to philosophers. I believe that it cannot! My reasoning is based on the notion that human consciousness or free will is actually rare in the grand scheme of the universe. From this I see no reason empirically why it must be esteemed, amplified as a force within nature that can still subdue nature. It might well be the case that consciousness is not very important as we are eager to claim. As Whitehead suggests the rarity of consciousness may mean that it is not that significant. The empirical evidence can lead us to either conviction but many are prone to divinize the human power of judgment, which I feel can be adopted as a matter of faith.
The interesting part to your question concerns the issue of indeterminism. Certainly, if one believes in a novel universe sustained through a creative advance then freedom is really shot through nature. Now I happen to believe in self-determination as the essential constitution of every entity under this type of categorical scheme. However, one could just as well conclude that freedom is not the property of man or any other beings. As Schelling claims, and Heidegger agreed, it is not we who have freedom but freedom has us! It seems to me these are plausible ways of looking at eternal or natural freedom. Out of indeterminacy emerge the determinate orders which are not governed by necessity. What we call necessary relations are sublated contingencies, developed out of the negotiated conditions of potentiality and actuality. I take necessary and contingent relations as possibilities unfolding through creative processes. Let me close by saying that this is a speculative endeavor, dealing with the metaphysical description of reality. It is not meant to be consistent with some process theology or school of thought, but with experience!