it might be confusing if different annotations and standards are used in different situations
That's a good point, but I think it probably applies more to the content of the file format we're talking about (e.g., the gene names) than the schema definitions themselves (e.g., the field "gene_name"). This file format will be "new", and there should be only a single, unambiguous way to refer to the fields that we define. That said, I imagine that referring to the field names in our schema will be relatively rare compared with referring to the content in the files.
I think your second point is more a matter for the germline team to decide. Whatever they go with, our file format will be able to represent.