As Sage say with Sage 50, "When you post journals to adjust the VAT Return you cannot reduce the values in a box, you must increase the values in the opposite box. For example, if you want to decrease the value in Box 1 you must increase the value in Box 4." (From https://my.sage.co.uk/public/help/askarticle.aspx?articleid=14697.)
A journal credit with T1, standard rate VAT, will always go to Box 1, a journal debit to Box 4. Not distinguishing between input and output VAT.
So, the VAT is correct, but boxes 1 and 4 may be higher than wanted.
How much of an issue is this?
An alternative which gurantees the right entries on boxes is: for output tax, to post invoices to a dummy customer account, or for input VAT, to a dummy supplier. Which also forces use of debtor or creditor control accounts.