The exported csv file fills the VAT return boxes as I expect and doesn’t include VAT on exempt items such as grant funds and CJRS. However, the auto populated values don’t match the export and include all of the exempt line items. Therefore reporting a higher figure to HMRC.
Exempt revenue items should be included in the VAT return as part of your sales figure. However, CJRS and grant funds are not exempt, they’re “outside the scope” and as such, should not appear anywhere on the VAT return as @Paul_Courtier says. You will need to check the VAT code you have applied to these receipts.