Same issue so I lean the bike back slightly and also use a hitch stabilizer. Have thought of making a little foam sock but once I was aware of the issue it has not been a problem. Cheap PA rack as well.
The part you have circled in red is easy two track and relatively flat. The 20% grade would be the three ascents after Mud Lakes to the intersection with the circled trail. So we came up from Mud Lakes, turned right and headed over to Yalakom. I was on a VStrom 650 with a burned out clutch so...
One thing to note on the Day 2 route - the KVR has an unpassable washout around Chain Lake/Shinish Creek Rd. In theory you get off on Chain Lake Rd and then rejoin somewhere around Jelicoe. Guessing it will be obvious.