Well, OK, thanks for the reply, but “resolved”?
The problem is: doing it that way does indeed break some module behavior, especially when trying to maintain customization compliance by using re-definitions rather than theme modification. As I mentioned, the comments in header.php warn against doing that very thing.
I fixed it the only way I could: put the calls back into the order they should be in, thus modifying the theme… which I was trying to avoid. Nothing failed after that change, but of course I am only concerned with my own utilization.
Just thought you should know; it seems to me to violate the standard.