Automatic harvesting only appears to work in Skirmish. However, if you set your war factory rally point to a tiberium patch, automatic harvesting does occur. I think that's standard behavior. I think automatic harvesting is a great feature (how RA2 works), but yeah, I agree having the default option would be good for those that want it.
Also, as I mentioned, alt+1-9 control group combo no longer works to center on units in SP. You can do do 1-9+F still, but alt+# is a bit faster.