Im sure that all B series spec R engine cylinderheads were polished by hand from hard-working Honda manufacturers. Not sure about the rest. But I remember saw in a video from best motoring the early days that somebody important from Honda said that only a hand build engine is the key to the high standards to a Type R engine. Couldnt find the video he said that right now.
Just the gate, where the molten metal enters the mould, would have been cleaned down after. I see the "hand built thing" more of a promo by Honda.
An example of a proper hand built engine would be the r35 gtr. There's a documentary on youtube that explains the whole thing. Very interesting.
I think Mr. Ichishima san from Spoon Sports knows the answer
at about 29 minutes he speaks about the engine.
He said that it took too much time by hand doing the porting job. So Honda decided to do it by specially designed machines since the late 1996 B18C-R.
So I guess they used the same machines to do it with the EK9 cylinderheads too.
Btw incredible how good the japanese test drivers were! By 0.001 the same 1/4 mile time side by side with the 96 and 98 spec R!