I rented with AutoEurope in MEL (to return in SYD). The actual rental was with Hertz, and to Hertz, it was basically a prepaid Hertz reservation. All of the actual paperwork and everything was done directly with Hertz--once I had booked my reservation, I was pretty much done with AE.
I would assume that would also be the case with AE in Europe. AE basically gives you a (digital) voucher that you use with an agency they contract with.
I don't know that I found out who the actual vendor (Hertz) was until I booked the reservation, so it kind of reminded me of a Hotwire booking...