The only time I rented from them was from the Haneda airport branch. I rented SP1 and ended up getting a GT86 when I went to collect it.
I would think branches near airports or major stations may be more likely to have the SP1 class.
As for specifically getting a GR Yaris, you may need to speak with Toyota after making the reservation to try and see if they can accommodate that request.
Last time I couldn't find any GR86 in Tokyo/Haneda, but found one in Yokohama... not even close to big station
And now I am looking around South-West area, and nothing available... no SP1 class