Re: Design & Build of Lanky - A Ozzie 8x4' long gantry router
If your Z axis has "fixed rails" (attached to gantry carriage) and cars move (attached to Z plate) up/down, then you don't have any stiffness penalty for increasing Z travel up to allow for tool length / tool holder length. Z can travel up above the bottom of the gantry.
Gantry walls / uprights only need to be as high as the maximum workpiece height.
IMO Z moving cars is better choice.
7xCNC.com - CNC info for the minilathe (7x10, 7x12, 7x14, 7x16)