Currently, the intercompany sales invoice to purchase invoice auto creation works a treat - you can map different dimensions and GL accounts and everything copies across perfectly, EXCEPT for the VAT/GST settings on each line. Currently you have to manually change them on the destination document lines.

VAT % is fetched on the basis of VAT Prod. Posting Group and VAT Bus. Posting Group from GL and Customer/Vendor. When intercompany transaction is done it simply brings VAT % from the combination in VAT Setup of the current company not from the sales document of another company. Hence, when creating any document for intercompany transactions, system will always pick the setup from master table of current company, not from the transaction table. We got the confirmation from MS Software Eng Manager. This is a product limitation, and the only workaround is manually changing the VAT in the target IC.

Ideally, the lines would take the settings from the source, rather than the above (or even better be able to choose in config what you want to be able to do.