Damn, that's true. I'm still working on my restoration project behind the scenes (away from the C&Ding eyes of Square) and that'd definitely conflict seeing how just about every field file is being changed in some way.
But with permission, authors could probably create a second patch that includes both their own work and the new backgrounds, no? Would you be cool with the idea once finished, sl1982? The releases would basically be like " 'SO and SO' patch merged with 'Team Avalanche's 2D Overhaul' ", providing immediate, obvious credit where due and alleviating any confusion.