I don't disagree but I think some of these problems could potentially be solved by having somewhat of a birds nest of a filesystem for large blobs, eg. /blobs/

I don't disagree but I think some of these problems could potentially be solved by having somewhat of a birds nest of a filesystem for large blobs, eg. /blobs/<sha256_sum>/filename.zip and then symlinking/reflinking filename.zip to wherever it needs to be in the source tree... It's more portable than hardlinks, solves your "source of truth" problem and has pretty wide platform support. Platforms that don't support symlinks/reflinks could copy the files to where they need to be then delete the blob store at the end and be no worse off than they are now. Anyway, I'm just a netizen making a drive-by comment.