I had the same issue and I fixed it by overwriting the function below in stock_move.py. You may customise it to return the existing picking under certain conditions (purchase order, sale order) in order to keep the standard Odoo behaviour and merge all pending pickings into one.

So far it works for me but I can't say yet if there will be some downside. Pls comment with your findings.

I agree with you the automatic merging of pending picking by Odoo isn't making much sense, one could use batches to treat many pickings in one go

def _search_picking_for_assignation(self):
    """Override to prevent merging pickings, but keep logic for potential future conditions."""
    self.ensure_one()
    picking = super()._search_picking_for_assignation()

    # Future logic can be added here (e.g., allow merging for sales orders)

    return None

Traceability back to the Source Document is managed in Odoo via Lot or Serial Number tracking of Products.