It's now been one year, and I can confirm that this bug still hasn't been solved. I'm currently using Karabiner Elements to remap ⌥ and ⇧⌥ to other modifier keys as a workaround for this issue. Recently, I decided to remove those remappings to check whether the problem had been resolved natively. Initially, the issue didn't reappear, but after some time—specifically after enough screen unlocks—the ⌥ and ⇧⌥ modifier keys combined with alphabetic keys started producing alternative keyboard characters again. This effectively blocks those modifiers from being used in key bindings. Apple, please look into this again. It's ridiculous that I have to resort to rebinding the ⌥ and ⇧⌥ keys in Karabiner Elements just to use ⌥ and ⇧⌥ keybindings effectively.