I have to say, I can see where you're coming from. In most places where Initiative is mentioned, physical initiative is treated no different from the other types of initiative, and merely lists the 1d6 without saying that it alone is increased by augmentations and the like (see p. 159 for example). The matrix chapter is especially bad; it says you get +3d6 (or +4d6) initiative dice, never saying this replaces, not adds, to the regular dice. With the whole "remember this can't take you past 5d6" blurb after, it's not a stretch indeed to conclude that that's on top of bonuses from wired reflexes.
But Jayde Moon gave the crucial page reference: the table on p. 101 says that only for meatspace initiative you add dice bonuses from appropriate sources. That's the correct interpretation, even though it could have been said more clearly in other sections.