I think St. Ansel would say that the Zones are what you see, not necessarily what the meter sees. The deepest shadows in which YOU see detail are Zone II. If you choose to put them in the middle of your film's range, that's your business, but they really should be very close to the bottom of the film's range for best quality. David Vestal refuses to call that thing we use an "exposure meter". He calls it a "light meter" with a calculating scale. It does not see zones. It sees what you point it at, especially if it is a spot meter. If you have it set to calculate for Zone V, you should point it at what you see as Zone V. Then Zones II and up should be recorded on the film in a printable fashion, provided you develop properly. If you cannot visualize the zones when you look at a scene, then use a meter that allows incident light measurements. Believe it or not, a little experience with such a meter and "normal" development will help you to tune your visualization to what the meter "saw". Often, just a comparison of spot metering and incident metering can be helpful.

As for filter factors, I think the same is true: try measuring with the filter in front of the meter and compare it with a measurement without the filter but adjusted by the filter factor. If the two measurements are in agreement, fine. Otherwise, spend an extra piece of film to find out which is better.