Yes, the log ends are flush, there is some variety in the notching with dovetail notch as the prefered technique. The logs are hewn on the inside and outside surfaces producing a uniform wall thickness. Often the inside surface was plastered again with lath over vertical furring. Certainly the siding and plaster work was done a few years after assembly of the logs.

On the modern siding issue habit, ignorance or a cost vs quality problem. I am also concerned that since the housewrap is a better moisture barrier the siding will suffer from direct contact whereas felt (the previous material of choice) will absorb water and moderate the water problems with siding.