Turns out having each server block share a single server.Config during initialization when the Setup functions are being called was a bad idea. Sure, startup and shutdown functions were only executed once, but they had no idea what their hostname or port was. So here we revert to the old way of doing things where Setup may be called multiple times per server block (once per host associated with the block, to be precise), but the Setup functions now know their host and port since the config belongs to exactly one virtualHost. To have something happen just once per server block, use OncePerServerBlock, a new function available on each Controller.
Even if defined for multiple hosts. Startup or shutdown callbacks registered by any directive (startup, shutdown, markdown, git, log, etc.) will only run as many times as it appears in the Caddyfile, not repeated for each host that shares that server block. Fixing this involved refactoring three packages (yeesh) and we need to restore some tests that are no longer valid (that used to verify splitting a multiServerBlock into multiple serverBlocks).