Tax accounting on project related intercompany AP invoices

We are implementing a tax rate to be generated on AR invoices from projects and in turn interface to AP as intercompany invoices. The tax accounts are getting defaulted correctly on the AR invoice but on the AP side the tax accounting is not defaulted from tax rate setup but it is derived based on the project details on the invoice item line. This is standard functionality for project related invoices  but we have a requirement to have different accounting for tax lines. Had anyone come across a similar requirement and aware of a solution? Please let me know.