"Interne" here surely means "within the group", not "within the company". On that basis the translation is right, because "inter-company" in practice implies "between companies in the same group".

Yes, if it is between companies within the group, or say business units /company codes within the same company.
If the German term describes that specifically then it would be all right.
But the term might still be misleading if left without a comment.
Usually "inter-" is contrasted with "intra-".

SOED: intercompany = made or occurring between different companies

I would not leave it this way, somebody looks at interne Verrechnung, and gets inter-company invoicing as result. That needs some more description / a better definition...