The incidence of the engine serves the same purpose as the thrust line.

It is necessary to know what you are trying to set up. If you want 2 degrees of downthrust, that must be taken into account. Unless the stab is not yet installed, normally, all measurements are going to be adjusted to the stab, because it is the only truly fixed reference point. If, on the other hand, you are willing to uninstall the stab, then it might make some sense to worry about the fuse.