Same target here for a testing project.
Research result: "Webkit Report engine" allows to design completely different layouts.
--> webkit-invoice Templates are available by community but free until the maximum of 2 users...

I can confirm a completely different Layout in Document Preview from RML Report Engine after generating a new company with no Source-Company.

Having generated a new Qweb-Invoice-report (http://www.askmpa.com/creating-multiple-invoice-templates-in-odoo-v8/) i see the following behaviour (v8):

• Report-Type "RML pdf" prduces the following error with or without webkit report engine:
  <type 'exceptions.Exception'>,Unhandled report type  

• Report-Type "PDF" uses the Layout of the first company, not as wished of the second one.

• Editing the view "report_invoice_secondcompany_document" to <t t-call="report.external_layout_secondcompany">
  Duplicating the views "external_layout", "external_layout_header", "external_layout_footer" to *_secondcompany 
  as well as adding according templates in addons/report/views/layouts.xml 
  --> should allow definition of an independent layout. 
  But it doesn't. By generating invoice following error occurs:
  QWebException: External ID not found in the system: report.external_layout_secondcompany

The only uncomfortable way to go is print invoices with one single layout and replace Headers and Footers via PDF editor until a solution is fount... :(