The short answer to this is yes 😁.
The Flat Rate VAT scheme is actually accounted for within your Xero or QuickBooks account, so you'll need to make sure it's turned on there, rather than entering the flat rate percentage within Link My Books.
Here are some links to how to set this up in Xero and QuickBooks.
Complete the Accounts and Taxes wizard using the defaults and your Xero/QuickBooks software will calculate your flat rate VAT based on the percentage settings you have added.
(If you have reduced or no vat rated products you will still have to pay VAT at your Flat Rate Scheme rate so there is no need to use the Product Group Feature.)