I need to bring alive this thread because I think there should be a way to integrate DLCs and updates into the base ISO. I mean, developers do it with GOTY, Complete and Special Editions, don't they? I am not sure where the problem relays on, but it seem to me it is the EBOOT.BIN file, right?
If the problem is the EBOOT, existing tools like "CFW Eboot & PKG Resigner v1.20 (x64)" and "TA Self Resigner" should help?