Cage:

How many times do you need to run this comparison algorithm? Does it need to be run every time one tries to transfer a morph? Can it be run once for each host and donor or once for each comparison of a donor to the host? If it does not have to be run often, why do you care how long it takes to complete its task? Just tell every one who uses your process that set-up time for each figure will take an investment of time.

Concerning Blender, Retopo is dependent upon the angle at which the process is viewed. Shrinkwrap is dependent upon the position of the target object and the object being modified.

Looking at the Shrinkwrap Modifier, it looks as if the distance between the target object and the object being modified can be set during the shrinking project.

If Antonia's head is loaded, and Victoria's head is loaded larger than Antonia's, the shrinking process can be done in stages, with the positions of either being adjusted between stages of the process. Would that make the Shrinkwrap Modifier more usable for what you want to do?

LMK

Probably edited for spelling, grammer, punctuation, or typos.