I talked to someone at C&A today about adding the upgrades to my preferences since you can't do anything on the new site now. They did confirm if you get "upgraded" to the Jr. Suite you do not get the 2 points per day because you are not paying the "suite" rate, but getting an upgrade, even when paying a little for the upgrade. If the price was right we would upgrade, but we did book a Jr. Suite for a cruise next year because the price difference between the balcony and Jr. suite was so minimal that we decided 4 of us in the JS as opposed to 2 rooms.
There is an option in your account settings to chose "automatic" upgrade or something like that.
I have booked over a dozen cruises with Royal and never received a call yet so I wouldn't get my hopes up. I watch for price drops and try to make my own upgrade but that doesn't usually work either.
Good luck and stay positive for the elusive Upgrade Fairy!