While I appreciate and understand all the sensitometry data involved here, I really believe the answer to Bill's original question can be expressed in less technical terms.
First, we haven't addressed one important factor in the ZS; that of adjusting development time to include a wide tonal range of 9 Zones (or 10, depending on how you're counting) for "Normal." This, I believe, is somewhat more range than the ISO tests result in. Therefore, a ZS N-development is usually less than the ISO standard development. This results in a skosh less effective film speed.
Secondly, we Zonies use our spot meters as arbitrary tools to place shadow values and see where other values fall. In practice, this ends up having very little or nothing at all to do with speed points or metering points (or middle grey for that matter). It is more an "I know what my shadows will look like when I place them in Zone III (or II or IV), because I've tested, and that's where I want them" thing. That coupled with "and now I have to adjust development a bit to get the highlight values where I want them" (many times callously disregarding the slight changes in effective film speed with shortened or lengthened development!) and we can consistently get negatives that are "in the ballpark" enough to be able to be printed well, even if we need to print a grade higher or lower than our target grade. For me, using the meter to help me visualize print values is paramount.
Furthermore, I think the Zone System emphasis on shadow detail and shadow metering, coupled with the relatively greater range of Zones and the resulting need to develop a bit less results in E.Is. that are slower than box speed for two reasons. First, is the slight bit of film speed loss with reduced development to accommodate more Zones together with the use of compensating developers/techniques, which also results in film speed loss. Then there is a tendency to place of the shadow values higher than might be done in the ISO standard in order to get "detail." Since no one takes up the Zone System without having a desire for richly-detailed shadows, and since most of them are shooting large-format film and aren't overly concerned about grain, there is a tendency in the entire process of determining a personal E.I. and then metering and placing shadows to err on the side of overexposure.
I know that when I test for E.I. and there is any doubt at all exactly where that Zone I density falls, I'll just rate the film a third-stop slower. What the heck, one third of a stop makes very little difference in the field. Similarly, if I'm not sure exactly where I want a shadow to go, I'll err on the side of overexposure.
In the end, a personal E.I. is not a film-speed determination, but an accommodation and adjustment of all elements of one's photo-making procedure in order to get repeatable and usable results in rendering of shadow detail. It only stands to reason that, consciously or unconsciously, we tend to err on the side of overexposing, thus building safety factors into our systems without even being aware of it.
FWIW, I shoot 320 Tri-X at E.I. 250 and TMY at E.I. 320, both only a third of a stop slower than box speed. This with PMK. So not all of us Zonies end up rating our film at half box speed. Even so, I'm aware that I've built maybe 2/3 of a stop cushion into my system. When the chips are down and I need a faster shutter speed to stop wind movement or the like, I won't hesitate to go ahead and "underexpose" my film by a stop (thus undercutting my safety factor). No one likes printing underexposed negs, but sometimes that's the only way to get a shot...