That just sounds like a bad application of the Zone System.
If one places the darkest shadow that should hold detail on Zone III, then one isn't changing the effective EI, because it still leaves room for Zone II "where nothing lives", as Sexton says, and Zone I, which is Dmax on the print.
If one places the darkest shadow that should hold detail on Zone IV, then I think you're right, but they are just compensating by one stop, usually for a film like Tri-X which has a longer toe, because they want to lift the shadows off the toe. In some ways this is just mental gymnastics for targeting Zone I for a density of .2 or some other value than Adams' original recommendation of .1, but that seems like a perfectly reasonable thing to do if that's the kind of film you're shooting.
I don't see it as a problem that Zone placement is in the mind of the photographer. That's where it should be, and if everything is tested properly, then what's in the mind of the photographer should appear in the final print. Isn't that the idea?
I also don't entirely agree with the criticism that usually comes from BTZS practitioners that the Zone System doesn't account for the characteristics of the output medium. It may not be very sophisticated, but that's the whole principle behind the density assigned to Zone VIII. If a Zone VIII density of, say, 1.2 on the negative, doesn't produce a visual Zone VIII density on paper with a given print process--i.e., the brightest highlight that holds detail--then one can adjust the target density for Zone VIII and development time accordingly. Perhaps this isn't so scientific as reading print densities from step tablets, but practically, it's not an unreasonable way to make printable negatives.