Sorry for the bugspam--wrong field:
I don't think attachments and notes need to be modified--there aren't multiple "legacy" formats that rely on a user-assigned identifier.
Customization of the algorithm would be an improvement. However (as you point out), having a "citation key" field seems to be the only way to reliably roundtrip data that is imported with citation keys.
BibTeX is the most commonly used citation format that relies on identifiers. However, OO.o's current citation database relies on them. And local IDs are used by the endnote and RIS tagged formats, so there might be other third party apps that make use of them.
