The pipe alignment is more or less set by where the engine rails are and where the opening in aft end of the fuselage is. Having said that, the more I think about this the more I still think this is some sort of thrust angle issue.

If I recall correctly the front end of the tailpipe ( engine end) is lower than the aft end relative to the wing chord line. To me that would equate to "up" thrust, I think ??