Phrenology has no actual science behind it, otherwise it would still exist in some way/shape/form.

Not clear to me what definition of "actual science" is operative here, and how you measure whether it still exists in some way/shape/form, but this may be hindsight bias.

Gall was taking real measurements inspired by:

- the faulty premise that there was a closer relationship between small differences in the exterior of the head and the brain than ultimately existed

- the ultimately borne-out premise that different mental faculties are closely related with different physical parts of the brain

If the science underpinning most but not all interpretations of fMRI results was debunked in the next 20 years, it seems like there would still be "actual science" behind the incorrect conclusions. How/where do you draw the line between phrenology's primitive grasp of the relationship between mental faculties and brain areas and the manifestation of the same concept in fMRI?

I don't think it's necessary, as a simple Google search on "structural brain differences" reveals hundreds of studies identifying physical differences correlating with various things such as transgendered individuals, dyslexics, etc.