You could certainly implement something with that function, but I think there’s probably no easy way to join 5000 VCFs in this manner right now – it’s essentially a data transpose.
It’s possible that doing a hierarchical full_outer_join_mt will perform adequately, as long as it’s broken up into ~2 pipelines (13 merges will be required to get to 5k, by log2(5000)), so doing 6-7 levels in each should work.