Yes it sounds like I completely misread the earlier emails, sorry about that. Now, looking at http://skarnet.org/software/s6/notifywhenup.html, I'm probably not reading that quite right, but it seems to tie the proposal to the 'notifcation-fd' file in the service directory, making it a bit less general.
The notification-fd file is for s6-supervise, i.e. s6's implementation of a supervisor. It is meant to make the fd number configurable on the supervisor side, to allow daemons to use whatever fd they choose. On the daemon side, you can use any option you like to tell the daemon what fd it should write to. It has nothing to do with s6, and I have no recommended policy for daemons.
s6-log however uses the -d argument to pass the fd, so I'll go with that.
-d works for s6-log and a few others of my programs. For others, -d is already used for something else, so I use another option. I really suggest you don't try to standardize a way to tell daemons what fd to use. No method will be universal, there will always be some obscure daemon that will conflict with it. -- Laurent