It doesn't seem to matter of the Intrastat option is checked or not on the Company record, Integration Manager throws an error when attempting to create a new Item in the Integration Manager. VAT10007 is empty but VAT10001 does contain records relating to Sites and possibly other mater tables.
The actual error is:
Microsoft.Dynamics.GP.eConnect: Number = 7997 Stored Procedure taUpdateCreateItemRcd : Description = The Country Origin does not exist in the Intrastat Maintenance table