As a summary of the discussion at
https://lists.gnu.org/archive/html/bug-readline/2025-07/msg00014.html
More generally, the inputrc settings are ignored for the characters
present in the tty settings. In general, both settings are probably
consistent, but for the kill character, there is an ambiguity: both
kill-whole-line and unix-line-discard match the tty kill behavior, as
in a tty, there cannot be characters after the cursor. Unfortunately,
bash/readline chose unix-line-discard (kill-whole-line is closer to
the actual description, so that this is surprising), and this is not
documented. In any case, whatever the choice done by bash/readline,
I suppose that a part of the users would prefer the other function.
The only clean solution to be able to override this choice (and
other tty settings, if need be) would be that the inputrc settings
should have the precedence over the tty settings. The readline
documentation does not explicitly say which one has the precedence,
but the intent, the logic and the practical usefulness seem to be
that the inputrc settings should have the precedence, which is not
the current behavior.
The only workaround is to set bind-tty-special-chars to Off in the
inputrc settings (e.g. ~/.inputrc file) with
set bind-tty-special-chars Off
In bash/readline, this was changed to On in the past (2005), because
some people complained that their tty settings were not honored, but
I suppose that under Debian, most users have standard tty settings.
Perhaps there could be some tests by Debian users. So I'm wondering
whether Debian should default this option to On.