Timing warnings...

Are you using OpenCore for IP? If these clocks are in the OpenCore logic (not in the IP itself or your design), then they won't exist in your final design after you compile with an IP license. If there are synchronous paths on these clocks, then the timing would matter for the OpenCore logic that enforces the timeout or requires you to keep the programmer tethered to the board, but I don't remember ever seeing documentation saying to constrain clocks like these. Application Note 320 says that "you can safely ignore" other kinds of warnings for nodes in the OpenCore logic.