With most of the sites we working, setting the number of threads to 10 (or more) really speeds up big sync operations and so on.

But some of the servers we work on have protection in place which considers more than 3 connections via SSH to be an attack and then blocks our IP for an hour.

It would be great if for these sites, we could override the global "Number of threads" setting on a case by case basis.

+1 for that. I have also problems with restrictions - some servers allows 3, some 5 and some unlimited connections.