Most common solution is to move the factory presets to the last three banks in the XL (D, E, and F) and then use the first three banks for your own presets. The MFC itself is limited to 384 presets, so it won't scroll any higher than that. However, you can use MIDI mapping to redirect any of those 384 presets to any preset in the XL, even past 384. You'd also still be able to access them by scrolling from the front panel.
Even if you remove them from the unit completely, you'll always have access to the factory presets through Axe Edit or Fractool if you download the .syx files from the Fractal website.