The thrust line as I understand it is the longitudinal datum line,
both horizontal and vertical, that the air frame desinger used
as the base from which he aligned the other components of
the air frame, most importantly, the wing, stab and rudder.
In aligning a motor you would like to know
what the designer had in mind so you can set the motor such
that it "pulls" as he expected it to relative to this line - and yes
this "proper" alignment may be ofset up/down/laterally and
alsom, very commonally, at an angle (in order to induce some right thrust).
Just my understanding. Hope it helps
Bruce