The discussion is heading in some unfortunate directions because of a
confusion between data entry -- which is a matter of the user
interface
-- and the underlying data _structures_, which are something else.
[...]
What's implicit in this is that Finale's data structures, like
Lilypond's, store the exact notes -- but Finale's _user interface_
permits a data entry method that simplifies the process of entering
tonal music, along with a number of macros to rewrite the underlying
data in different ways when key signatures are changed.
On the other hand if you're writing Lilypond code using a text editor,
you're writing straight to the underlying data structures used to
generate the score -- and it would be insane to distort this with
'follow the key signature' rules, because it introduces all sorts of
recursive dependencies and potential sources of error.