I have bank transactions for a VAT refund and a VAT payment showing on my Aged Payable report as 'Unknown Partner' transactions because they have nothing in the Partner field on the journals, therefore I can't reconcile them. Do I have to set HMRC up as a Vendor, which doesn't make sense, or is there something I've missed in configuration?
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If you define the account type of an account as account receivables or account payables, then you should use customers/vendors as partners. You can also do that with HMRC, but AFAIK usually you do use separate accounts of type current assets, current liabilities respectively.
In ths case you post/reconcile directly to the corresponding acconts. Check your tax configuration, your localization and ask your accountant.
