Just for fun, have you tried different
Physics.Raycast(...)overloads?
@Senshi - Not different overloads, but all these: Physics.Raycast, Physics.RaycastAll, Physics.RaycastNonAlloc, PhysicsScene.Raycast
Are rays has the same crossing Point? Is it a upper sphere center?
@szynal - They all intersect the edge between the lower hemisphere and cylinder body. I have a photo in the original post to show this.
If you have not yet submitted a bug report, please do so.
@Arithmetica - Yep, have done.
Make a blank project, type in your numbers, report it.
@Kurt-Dekker - I have submitted a report through Unity with the contents of the zip above, additionally I have linked in the report status page back to this discussion thread as I have found more info since. Hope this is enough.
More so if anyone is really concerned about this bug, it should mean you could augment the capsule with additional 2 spheres.
@Noisecrime - That is one solution. I have done only simple checks but only adding the top sphere should be necessary, the rays correctly hit the bottom hemisphere.