OK I came up with an idea that should work : I added bicycle=no to bar access for bicycles to cross kipling at  41st.  This should tell routers to take the long way around through the underpass when traversing clear creek trail.

same caveat still exists - though OSM sourced maps should pick up this change and no longer route bicycles across 41st.  Hopefully this solves the issue -- I assume the 40th intersection should be OK as it has pedestrian sidewalks...