If I, for instance, have 75 files in the file window (under a collection), many of which having the same file name, I can auto-stack by the file name to group them... Very handy!
However, in order to propagate metadata between the files in the individual stacks, I first have to create a manual version link. Is there any way to do this on auto-creation of the stack in the first place?
I assume you refer to Commands > Relations > Auto-Stacking (https://www.photools.com/help/imatch/rel_stacking.htm?dl=h-10)?
Auto-stacking creates regular stacks, not version stacks. These stacks don't support propagation.
IMatch propagates metadata from the master to it's versions. Versions form a version stack automatically.