WYKP?
The steel rod should be as far down in the cylinder as practical. This is because the OEM and most aftermarket pistons have piston pin offset, and the piston movement in thousands of an inch per degree of crankshaft rotation will differ slightly between BTDC (piston rising) and ATDC (piston falling). This difference quickly becomes insignificant as the piston goes lower into the cylinder in either direction. 1/8" down: big error, 1" down: much smaller error.
The rod's motion may be suspected as a method of measuring the piston's motion in thousandths. It is, and it's linear (directly proportionate), but not equal (unless the spark plug thread is exactly vertical/parallel to the bore axis). The rod will always move faster than the piston, by the cosine of the spark plug thread angle in the head.
If someone knows what that is, I will write and post a chart of plug thread rod position vs. actual piston position.