Just looking at this Experience Cloud documentation for the first time LWR - Differences in Behavior and it looks appealing where you want to build all of the UI yourself to have fine grained control, and also pick up performance benefits.
We have some existing flows that are primarily used to allow additional processing steps to be introduced i.e. each flow screen corresponds to an individual LWC with the flow conditions primarily determining where to go next.
Am I correct in assuming that these two things do not fit together today?
This video reviews Building custom navigation and footers for LWR sites explains how to leverage some of the declarative parts of the builder and incorporate that data into custom navigation. So offers a bit, at least for entry point pages.