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Technically it is possible to add both a ligature in the common form of "f_f_i" (and its accompanying Feature code) and a separate Unicode glyph for the same character -- U+FB03 for "ffi" -- to the same font.
Is this a good idea? I'm pretty sure it's not!
I only tested this with InDesign, but I vaguely recalled that it would automatically use "fi" and "fl" ligatures, if a font had these characters in the correct Unicode positions. However, a quick test with a freshly created OTF font shows it does not (in CS4, at least). Perhaps this is (or was) only true for Plain Old Type 1 fonts without any further OTF enhancements.
Regardless: if I add both an "f_f_i" glyph and an "ffi" Unicode glyph to a font, what sort of issues would I encounter? Maybe all it shows is in what order the underlying software examines ligature candidates. Some might first parse OTF features (which -- again, I think -- would be preferable), where others might check the character map first.
Or maybe the entire font drawing machinery crashes.