There's just no getting around it. If you place one of our z-independent under-the-gantry dust boots (atm v2, v3, and v9) onto your CNC machine you WILL loose some of the machines Z capacity. We've went to great pains to r keep this trade-off as minimal as possible.
First off our boots immediately under the gantry are roughly 1" tall. After passing the gantry we do swoop up to accommodate our proprietary boot adapter receiver.
We ship these boots with a 1" brush as standard. Thus our boot+brush takes up about 1.8" or so (brush is recessed slightly) of your overall Z capacity (that distance between the bottom of the gantry and the top of your bed).
An easy example I can make is with my Shapeoko Pro (default configuration, pictured above i've installed the 3dTec risers for increased capacity) you have about 3.75" of available Z capacity. Since our boot takes up 1.8" or so you can reasonably carve stock just shy of 2".
I'd say 90% of folks sporting v2/v3/v9 aren't cutting anything thicker than 1" or so.
If you're cutting something >=2"... this is exactly why i came out with v4. So you loose NO z capacity and still get to enjoy the benefits of a z-independent boot.