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I'm pretty there are applications where ctrl/alt would be useful. emacs would be one example (it has gtk support, does not always run in terminal...). But yes, terminal is best example.
I'm glad that you mentioned a non-terminal example, because it forces us to consider that ctrl/alt are not something limited to the terminal layout (and so the input hint loses a lot of its purpose).
What I meant when I said that no other application (okay, use case) needs a real Ctrl key is that the feature is not necessarily trivial to implement in the input method. When using text-input to enter text (as a well-behaved input method should), then there will be no code to support modifiers in the input method at all. The input method will still be 100% touch-functional, because no application that doesn't carry historical baggage of physical keyboards will ever need modifier keys.
In philosophical terms, I'm not 100% sure whose responsibility is to provide for such a quirk. I guess for the time being, the keyboard could do it...
I think a terminal input mode somewhat implies the ability to do things like ctrl so from my non-im perspective it would be odd to GTK_INPUT_PURPOSE_TERMINAL and not get ctrl along with fn keys etc
If we take input purposes as the ultimate source of truth, then yes. There's still value in considering other arrangements, like some "NEEDS_PHYSICAL_KEYBOARD" purpose which would request an emulated keyboard for any application that doesn't support touch interaction properly.
Here I'm hinting at one view of the situation: if some functionality requires a physical keyboard (amulated or not), can the application be considered touch-friendly?
bash is not the application we're talking about though; the user interfaces to it via the terminal emulator, and this is the part of the system which can accommodate for the user.