If you need GO annotations for Ensembl genes, just get them from Ensembl for the specific version you're interested in. You can do so using BioMart or the API. Uniprot-GOA is not concerned with a reference genome, it annotates protein sequences and other resources like Ensembl do the mapping to a reference genome. So if you want to use GO terms associated with some Uniprot IDs and need to map those to a particular reference then just find which genes the Uniprot IDs are associated with in the reference genome you're interested in.