He's using G54 to define a repeatable reference point for the probing cycle, and then G55 to define the stock offset relative to that known reference point. How the stock is positioned in the vice is kind of arbitrary unless he set up a stop or machined a reference ledge in softjaws. Since G54 is defined by static geometry (the vice jaw), it's not going to change part to part. That is nice because once you find that, you don't have to touch it again. Then as you work through your run of parts, the probe is starting from the same reference point and updates G55 based upon however the material is installed in the vice. If the probing cycle overwrote your initial G54 every time and used that for the toolpaths, then you would run the risk crashing the probe if the stock is installed beyond 3/8" of an inch out of position, in this example - since the new baseline for the next probing cycle would have the offset from the previous part entered in. Say part 1 is installed 3/8" to the right of center, it gets probed and machined, then part 2 is installed 3/8" to the left of center. The second part would get probed 3/4" off of its true physical center (since the probe is referencing G54 from the previous part) which can't be compensated for without putting in a lot more over-travel.
