I answered my own question. For continuous replication, delta's are automatic. I was thrown by a backup job where I mistakenly selected disaster recovery instead of continuous replication and didn't realize it.
@RKENS Good question, during the replication, a new VM is created with the same settings as the original one, and this at every run. Therefore that's perfectly normal that this property reappears.
I don't see how that's a problem because, as you said it yourself, the start operation is disabled by the replication job.
I think it makes sense that the auto start is set like on the original VM so you can simply start the replication when necessary without having to think about enabling it.
Your CR issue might be related to a XO bug on master, not too a XCP-ng issue 😉