I also repaired the rust spots in the tailgate the same way. I removed the handle and found another water leak in this process, this time in the left most handle's bolt. Here's some shots of nut holding it and the rust that formed on it and around the bolt and tailgate opening. This was a slow and active leak, where if left unattended would lead to a nasty rust repair done by a shop. I didn't know it was present until I took the tailgate apart, but I'm sure glad I found this now!
I recommend taking the tailgate plastic off, 2 7mm screws in the first aid kit pocket, and a 10mm bolt at the pull down handle, pull out that handle pocket, rest is snap on clips, have the glass open so you can pull off then slide the plastic cladding up and off the window latch. Peel 2 sound deadening plastic bits off the tailgate. Easy.
It hadn't rained in a few days, but I did have some drips of water pooled on the deadener:
Here's some pics of the tailgate after removing the handle, which was 4 10mm nuts and then 2 snap clips holding it in place. Unplug the connectors for the unlock button and trunk release switch in the handle.
With the handle removed, I sanded down the rust spots very carefully with small sanding wheel on my dremel, removing the rust to arrive at clean shiny metal, primed, and painted. I also then applied thin strips of 3M Automotive double sided tape in these spots so that the handle will never rub the paint down ever again.
I used my dremel to sand down the offending spots just a little to accommodate that 3M tape, about a mm.
Since I had a water leak in one bolt, I also added some rubbery foam stripping over each of the 4 bolts and then silicone greased around those 4 bolts for good measure. These things should never leak and it annoys me to no end that something simple and preventable with a quality gasket wasn't done. My 2 cent fix here will do it.
Finished product, visible if you crouch down under the tailgate handle to look at. Some fiddling may help tidy up the 3M tape a bit more but you get the idea. No more rust here.