Spoke to the distributor. Here's the scoop.
The GIPro fools the ECU into believing the bike is in 4th gear. So with my 20226 tune, the secondaries will not be affected as they are opened the same in all gears at all rpms but the ignition mapping will adjust accordingly. The tech stated that the opening of the secondaries is a side benefit but the main focus of this unit is to adjust ignition mapping.
Therefore, I should still receive some benefit but will still need to remove the secondaries to unleash the complete beast. I'll be putting the GIPro on without removal of the secondaries and report any differences but it'll have to wait for better weather. F***'n cold up here!