The question about tolerances on the pier is a little tricky to quantify. We’ve been using aluminum as extrusions can be very stiff, lightweight and pretty inexpensive. Its also used by vendors who make commercial mounts. It does expand as you point out and we never tried to intentionally minimize this as the expansion is most likely negligible and would be hard for us to observe. Note that there are many other parts that are also exposed to the out door temperature including the mount, the dove tail rail, the enclosure, and to some extent the cameras on the mounting plates. How all this moves with temperature is pretty hard to model especially as we track a field. While we track we see small motions of the star across a few pixels do to imperfect alignment and guiding errors and my guess is that thermal expansion for the current pier is absorbed in this observed motion and challenging to extract.
What I would say is that if you find wood with a thermal expansion coefficient within a factor of 2 of aluminum, its probably good enough. What I was more worried about was twist type deformations. Soft wood can deform by a lot more than thermal expansion allows so I was basically advising to make sure that the hard wood you choose does not deform significantly (based on what people say online). This would be worth testing in any regard.
Once the unit is mounted at a site, and polar aligned, if it is not moved there is no need for a re-alignment. Our other units dont drift. Again, we do see star motion from many effects so unless we see something changing with time in a particular direction, we dont re-align. If you did observe warping of the pier beyond normal limits, then yes you could polar align again if needed.
Interesting idea about water proofing. Our unit sits at MaunaLoa where the annual snow storm will dump plenty of snow and the heat from the electronics in the control box have been sufficient to keep things at a comfortable temperature. Im not sure how they would work in extreme cold for long periods. Insulation might be needed.
My suggestion is keep it simple. Id start by building the unit and getting it going. Then if needed upgrade things like adding insulation for example.