Hey there, yes, the car did indeed have a factory installed spoiler.
Currently, I am running both a rear wing AND rear lip FD2 Mugen RR combo, they're two separate pieces that SHOULD fit together on the trunk.
Now, the rear wing fits very well without any major problems. The two vertical 'towers' should line up and cover the OEM spoiler mount holes, even though the shop where I had the car worked on filled those too.
The problem is getting the rear lip to sit nicely as the CG2 trunk curvature differs from the FD2 trunk curvature in all 3 x, y, and z axes. The shop had to heat and glue the lip to sit well.
You could very easily omit the lip and just run the wing, but I think the lip rounds off the Accord trunk very nicely. Are you considering the wing/lip yourself ?