That's incorrect.

You are thinking of the older way, where fcntl(fd, F_SETFD, FD_CLOEXEC) must be used after open(), leaving a short window in which the file descriptor may be inherited.

The newer way passes the O_CLOEXEC to open() and there is no fcntl() call. This is atomic with respect to inheritability: The kernel returns a non-inheritable file descriptor to libc, and libc returns it to the application.

Other syscalls that return a file descriptor have similar flags, so they are atomic too.

These flags and behaviours are exactly the same, whether done by calling through libc as most programs do, or direct kernel syscalls bypassing libc, as Go and a few other programs do.