I have always found the gps indicates less speed compared to speedo, in my 3 recent rides.
I have 3.4% larger than stock wheel diameter on my pkdm vigo, and still the speed is 6% less (94km/hr vs 100km/kr) on gps.
My 8th gen civic had about 5% difference (stock wheels), and not sure about exact %age on 9th gen, but I do recall that in cruise mode on M2, with slightly oversized wheels, the difference was still about 5km/hr at 130km/hr speed.
So, its not a biggie, and pretty normal to find an inaccurate speedo. I take it as a good reason to install slightly taller tires (wider tires with same profile %age).