Yes, many practitioners (myself included) of the Zone System have adopted bits-n-pieces of it for one's own use. None of this negates its usefulness or principles. Fred conceived of many new ideas that were quite controversial at the time. For example, MPD (maximum printable density) which stipulates that you expose for Zone VIII, then let the shadows fall where they may. Fred's theory was that you exposed and developed for the most density you could print. This, of course, ignores minus development, but Fred never agreed with minus development and he liked to keep things simple. I used this technique for many years, but later in life I started working with staining developers and minimal agitation techniques that somewhat negate the need to worry about the high values. Additionally, new films have been developed (pardon the pun!) over the years that have a much straighter curve allowing the high values to separate better.
I totally agree with David regarding the placement of shadows in Zone III or Zone IV. If you've tested your film for personal EI and are careful about properly metering shadow areas, then placing these areas in Zone III shouldn't be a problem.