Is there a utility I can run that will recognize which app is in the foreground and perform auto-key translations from what I type to what the app expects?
Certainly not. The industry actually makes money by selling certificates and by changing designs, so "your average user has no clue what's new, and your expert requires a new cerificate and may experience difficulties with the new menu structure".
An Open Menu design would be better, in theory. If you believe that "Exit F4" has nothing to do with the "File" of its menu, then you can channge menus and define other keys.
You will have to hack (all) apps. If you are using WordPerfect for DOS to manage old documents and press Alt-F4, then what should happen?
And you will have to manage your own database, to define what you'd like to use and what apps should expect. Without any conflicts.
I'd like to use Ctrl+C, Ctrl+X, Ctrl+V for Copy/Cut/Paste, and I have a dozen other keystrokes I'd like to use rather than the ones in the OS/2 apps.
Those keystrokes may work too, with more than one OS, and I presume it will be easier to contact authors of apps to change assigned keystrokes. I wouldn't consider customized changes for one user, though. Unless it's a quality improvement, like supporting both Ctrl+V and Shift-Insert.
I guess different keystrokes may account for over 50% of the existing editors (vi, ...) and file managers (Norton Commander, ...).
The last version of MS Office for Win-OS/2 does offer the user a few optional different keystrokes of that era, like IIRC the "/" of Lotus for DOS in Excel or w.r.t. Alt-F4 of WordPerfect for DOS.
"Dynamic Keyboard Remapping" won't be worth the extraordinary efforts, if it's possible at all. "Esc" doesn't always escape, and so on.