I note your top screenshot shows Reopen Last Closed Window as Control-Shift-S, too, which certainly suggests something is amiss with your setup. I don't think it's on Apple's end, as that command, when relevant, shows up in the History menu for me as Shift-Command-T, as expected.
It might be worth disabling your third-party stuff if possible, or booting into Safe Mode, to see if there's some kind of conflict going on. (It's not too hard to imagine that something's different in Safari 10 which doesn't play nice with previously compatible software.)
OK, I've now got more of a handle on what's going on...
- Sometimes Safari 10 launches to History > Reopen Last Closed Window > Control-Shift-S, and sometimes to Reopen Last Closed Tab > Shift-Command-T. (I haven't been able to pin down what governs that.)
- In that state, the displayed command works more or less (*) as expected, and Command-T opens new, empty tabs as expected.
- As long as I stick to opening and closing windows that state persists.
- Once I open and close a tab, the command changes to Reopen Last Closed Tab > Command-T (*), and in that state, Command-T works as described, not as expected.
- If I then open and close a window, the command reverts to Reopen Last Closed Window > Control-Shift-S, and Command-T again works expected.
- Once Reopen Last Closed Tab > Shift-Command-T disappears I never see it again, no matter what I do.
(
*) When hit repeatedly, whichever command is in play successively reopens both previously closed windows and tabs,
BUT what's opened isn't limited to current history, rather windows and tabs that had been opened in a previous Safari session whose history had been erased when I quit Safari are also reopened, which strikes me as a security breach, perhaps even a critical one...new in v 10.
I've now tried disabling my extensions, booting into Safe Mode, (even) repairing permissions, and d/l'ing a new Safari 10 updater (in a different volume), all with no joy.
I've booted into a clone running Safari 9, and found that Reopen Last Closed Window > Control-Shift-S is the default command, and, without going into details, it works coherently and as expected.
Control-Shift-S is not listed as a command for any Safari function in either v 9 or v 10, and Command-T shouldn't have anything to do with reopening previously closed tabs, so I've got two spurious commands (one going back to v9), and that's with no conflicts between my third party hot keys and any of the Safari commands I've mentioned.
Since, as I explained
here, I can't rerun the 10.11.6 Combo to revert to Safari 9 I'm stuck with this situation unless I do a clean install or upgrade to Sierra (which may not even help).
Any and all thoughts, suggestions, and wild guesses happily entertained.
