I had no luck to merge same data existing on 2 sync clients. Most likely because of time difference NC decided to use one side and synced all the data (even it was same).
Based on this experience I would suggest just to select your source, sync the data to _Nextcloud> and later sync all the clients from there. Definitely syncing consume CPU and bandwidth but AFAIK this is the most predictable solution - you know which data you use as source to feed your server and this way you distribute the same data to other clients.
I have the same configuration than you (if I understand correctly) : 1 server and 2 clients. And I think I ended up to a similar solution than yours : 1 client 1 server sync, wait until server is happy and then add second client.
I’m still in the process, we’ll see with what I’ll end up with.