I would be interested in seeing your scene in OV and see details about the perf you are seeing. Maybe you could join our discord server and share it there? Without more information I am not sure what the reason is, but I can imagine 2 things:
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OV does add overhead so if you are comparing using FLEX as standalone vs PhysX 5 in OV, its not expected to be the same, even if you are talking about the same simulation feature.
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PBD Particles are not the same as FEM! Flex (at least more recent versions) had both FEM and PBD. FEM is a much more expensive and accurate way to simulate deformable bodies. So the perf will be, even independent of OV, be lower with FEM. PhysX 5 will have both features, but particles are not ready yet – in fact both features are still under active development. What you see today is just a very early first version.
We’re working on improving OV perf.
(See: Omniverse Discord Server is LIVE! for discord.)