Well esthetic energy and giant monsters are obviously a fantasy element but it appears to generally be amenable to a set of regular laws and other physical principles seems to remain in effect. Therefore one would expect general atmospheric structures to also exist. Like for instance a structural thermocline could easily explain the mist layer. As for the rust problem I assume that is an interplay between the conduction of eathric energy and high atmospheric moisture.

It seems to me to be implied that the spire touches the ground and that all habbels are above ground level when Addison tells Grimm that he expects POW's to be sent down to work at the base of the spire.

With regards to altitudes and atmospheric mixing it can be as one poster mentioned a little complex.

The FAA requires suplamental oxygen for the minimum flight crew members opporating at or above cabin pressures altitudes of 12,500' MSL for 30min or longer. Minimum flight crew operating above cabin pressure altitudes above 14,000' MSL for any time. All occupants above cabin pressure altitudes of 15,000'. (14 CFR 91.211) now obviously there are people who live much of their lives above 2miles and some people are living a fair bit higher then that. I have personally spent a good amount of time (months at a time) higher then 11,500' and have climbed above 14,000 on numerous occasions. In general anyone can acclimatize to a wide range of altitudes initiall acclimatization taking about 48hrs and full acclimatization taking something like a week. However somewhere around about 18,000'-21,000' (if I am recalling accurately) you start to see metabolic efficiency drop off and people litterally starve to death. So assuming modern earth like atmospheres we could allow for the lowest levels of our two mile soup can to be as high as a mile and a half above sea/surface level.

When it comes to atmospheric mixing there are two or perhaps three main variables depending on how you want to distinguish between them. The first is water vapor which is incredibly variable in our atmosphere. The second is temperature profiles also quite variable especially in lower atmospheres. There tends to be very little mixing across a couple of boundary heights due to the interplay of these two factors. When I am reading the books I tend to think that the mists represent one of these structural boundaries perhaps analogous to the tropopause but existing much lower in the atmosphere. The third factor are Hadley/feral cells which do mix the upper and lower atmospheres.