I've done a few log projects with a local log builder. You will likely find that log construction is a true craft and that each contractor has strong preferences and style.
Punched Openings:
The contractor who I have worked with prefers to leave the settling allowance at the top of punched openings. Windows and doors are secured to the log walls on three edges only (bottom and sides). The bottom connection is typical of wood framed construction. The sides of the windows and doors are fastened to a small steel angle; one leg of this steel angle is fit into a groove that is cut into the logs. This secures the window from out of plane movement while allowing the logs along the sides to settle downward without applying load the the window or door. Finally, the top of the opening is fitted with a dimensional lumber buck (girt), the ends of which are secured to the steel slip angles on the sides. The window or door can be fastened to this girt. Above this is the settling allowance space, packed with a collapsible insulation (sheep's wool or loose fiberglass batt). The settling allowance is approximately 3/8" per 12" dia log, but can be calculated easily. Wood trim is fit to slip over the window as the logs move down.
I usually get the architect to detail these openings. I detail my punched openings to have the appropriate rough openings and let the architect detail all the vapour, moisture, and air barriers, insulation, etc. It's a complicated area.
Settling of the structure is an important consideration, especially for columns, stairs, and finishes. Columns will not settle with the log bearing walls and therefore need to be placed on screw jacks at the base. A maintenance plan needs to be in place to monitor downward settlement and adjust these jacks appropriately. Stairs are up to preference: often the settlement is sufficiently minor that the stairs end up slightly tilted positive after settlement (and often remain within my buidling code tolerance of 2% slope for this). Finishes need to be carefully planned to allow trim to slip over fixed items as the building settles/shrinks. Demising walls need to have sufficient settling space left above them and a slip connection at the top.