Ha that's a good one yeah I don't think I've ever seen a neutral scout, either. Technically they don't do anything for you so not the kind of bot people would build or hack.
They become neutral because they don't have any offensive combat AI, which is what the Programmer uses to set their faction on assimilating them.
I was going to leave this as is since it's not really a factor, but I guess I'll just treat it as a special case and have them put Watchers in the combat faction where you'd expect them to be