With respect to the original question, your observations are the same that we all see upon disassembling a lens for service.
The positioning of the parts is determined by the maker. Thereís no adjustment possible, except for indexing the actual focus relative to the position of the focusing ring on helicoid-focusing lenses.
Itís possible in some cases to incorrectly reverse the orientation of individual elements. If the element is asymmetrical, the optical quality of the lens is spoiled. This could easily happen with a double convex element with slightly different radii of curvature on each side. It might look symmetrical to a cursory examination, even though itís not.
Reverse it and the lens wonít function properly. Too, the metal surfaces on which the element seats against can damage the glass and coatings if reversed because the shape of lens and seat are not mirror image as intended.
My first helicoid CLA was to a 50/2.8 Zeiss Tessar. I used lithium grease. The turning resistance was so great that I almost needed pipe wrench to turn it. Vaseline (petrolatum) is too dense for most focusing helicals. I then replaced the lithium grease with this.
The focusing ring now turns smoothly with the resistance Iíd expect of a new manual focus lens.
For AF lenses or manual focus lenses intended for arctic conditions Iíd use this.