Yes exactly. A combination between RF shielding layers which double as heat sinks plus a soft heat conducting layer for internal dampening (thermal adhesive layers - I buy sheets of them for my water cooling mods), and 3D printed PLA or ABS to hold it all together (actually with non-conductive layers in-between we could probably make a design for people to DIY without 3D printers). Probably with integrated gimbal ball base as desired (easy to add or remove when it’s a 3D printed model).
The cold air from props and movement along the side will draw all the heat away from the barometer and other chips. Also cooling on both sides of the Pi, and potentially cooling the Navio although I’m not aware of any heat issues with those types of sensors (perhaps only the PWM chip?).
The Pi Zero already has the pins removed, and there are examples of people stripping the ethernet, HDMI and USB ports off the full PIs. The Navio pin receptor is quite low profile already so maybe for the sake of keeping the warranty on the most expensive item we should not attempt to remove that.
Perhaps my quick diagram has too many heat sinks (could do away with the ones along the top. It’s difficult to express the whole length of the design in one cross-section. Smart placing around the components would obviously be done. It looks almost as big as the full version in this quick diagram. I really mean super compact, super low, just slithers of material between the components (as thin as effective = needs experimentation).
Then of course we can vary this design, with the PiZero flat, and also sticking-up vertically or to the side like a T (one row of pins connecting to top and other to bottom of Navio may also be neater). Depends on the drone frame design and the overall results to heat disapation and shielding (the flat one most likely being the best all round).
p.s. of course we cannot completely cover the barometer chip and LED. All these limitations need to be factored into the design.