This subject was discussed a couple of years ago on this board. Specifically dealing with the outboards on a 727. I know that some real smart, well educated, aero engineers offered a good answer. Maybe you could search for that.
Off the top of my head, I think that the thrust line is determined by quite a number of factors. How the thrust interacts with CG and with the aerodynamic center, affects the proper placement when considering aircraft stability. The thrust line placement affects how much pitch changes in relation to power changes and therefore the trim authority and speed requirements. I wish that I could relate exactly how all these factors interact, maybe someone will jump in. What I am fairly sure of is this. What you see is the result of a compromise. The designed thrust line is the best combination of: cruise speed efficiency, single engine controlibility, trim requirements for power changes, proper airflow into the inlet, and many more.
regards, 8N