Major problem I see is that the series would end early through some of that stuff, or need a complete plot rework. For example, if you destroy the unbound at the end of gf4, the rebellion is fairly done for, at least by the ending there. Would be great though if it could be done well (perhaps in moderation, so not with the major endings, but some more minor stuff like you suggested about the gf3 shaper's name).
I'd rather see more Geneforge games in general than that though Avernum has the second trilogy, how about the second Geneforge trilogy or quintology? Playing through them again recently I remember reading that Terrestia is only the second shaper continent. And never mind the Sholai lands.