Is anyone able to share a best-practice “fully landed COGS” SOP to ensure that all costs components like production, freight, labelling, etc etc make their way into COGS, even if some of these invoices arrive late?

Your truly landed COGS is fine if invoices are late. Most companies will not bother using estimates (then washing them out when actual bills come in) because it is too much effort to wash out the estimates. You can run your true fully landed cogs with late bills, you will just be lacking reporting insights as you wait for the bills.