Yes the touchdown zone is for instrument approaches and Pref A machines as are the PAPI's.
A 3 degree PAPI approach is just as inapproprate for a light aircraft as a light aircraft profile is to a 747.
I fully understand that a light aircraft following PAPIs is not going to land at the same point on the runway as a 747 but, as a principle, I see no reason for ignoring aids put there to assist approach and landing. If there is a 'proper' TDZ the runway length will almost certainly not present challenges for light aircraft.
A farm strip is a different matter altogether, and that's why knowing how to touchdown where you want is an essential skill.
Things like bomber circuits and landing long to help ATC are completely different subjects.