There are several different STD castings made. Some have much larger fin surfaces and others are designed to look more like OEM heads. Regardless of which type of casting you have, the rocker box height should be the same as OEM.
STD first came out with a replacement Shovel casting. They then modified the shovel casting to accept Pancovers and internals keeping the shovel intake and exhaust flanges.
These castings do not look at all like true panheads.
I have STD heads on one of my bikes. You should not be having any trouble with fitting the motor in the frame. Like VonWegener said they are totally different looking but 75% of the riders today have no idea what they are looking at and I noticed that at 80 mph even a greater group cannot tell. Good luck enjoy the ride.