Perhaps, but for all we know said Runabout had NCC-1701-D/R2 or something pasted on the side. All we saw was stock Rio Grande footage and a couple new shots which had no visible lettering. In any case, no TNG-era shuttles had any /# seen, just the mothership's registration.
Didn't New Frontier have a Runabout assigned to the Excalibur?
Mark