I don't think it does, but I can certainly test it... All I know is in the specific case of MINIMAP:PingLocation, the ping only happened on the little circular minimap, which caused your mid-cast AoE spell to target that location. The actual coordinates fed into Minimap:PingLocation were indeed relative (I recall doing something along the lines of 0,5 ; 5,0 ; -5, 0; 0, -5 on my warlocks to cast my anti-rogue rank1 rain of fires all around my location).
If it was indeed relative then I concede on that, I thought it pinged a specific location. And if it doesn't do it with a manual ping then yeah, it wouldn't matter about replicating clicks on the minimap, and the question would revert back to whether or not it matters where the click is.