Isn’t this what CloudKit data sharing (I tried to include a link to the relevant documentation but am apparently forbidden to post links) is for? I think syncing with multiple IDs is possible under CloudKit. Bookends does it successfully.
I’d also add that I’d really like to see this feature in DevonThink. I maintain a separate iCloud account for my work machine in order to separate work and personal materials. I’d like to be able to share certain databases with my work iCloud account while keeping other databases not shared. Again, this is something Bookends manages—I am able to share some of my libraries while keeping others only on individual iCloud accounts. So this does seem to be technically feasible.
Right now I’m managing to make my setup work by using Dropbox to sync with my work machine, but I’d really like to be able to do it all with iCloud, and CloudKit sharing seems as though it should make that possible.