But as far as the Open Source indemnification goes - for the Android Auto use case it would be completely irrelevant right? That would be like suing Vizio for showing a pirated movie on the screen as far as I can tell.
For using AOSP - I can see that there may be some reservations there. But it is not unprecedented - Honda I think is using Android 4.0.4 to run their in-car system. Besides the biggest threat to Android from a patent / legal standpoint is Microsoft. Worst case Ford would pay up the $5 or whatever and still win on not paying QNX and having a better solution.
As for the dependencies / ecosystem - they could still support the older released models and start working with vendors/suppliers to get what they need supported on the new system. It's doable because presumably with the new Architecture - most things are either built in or you don't need those and people already have experience building what's missing. For example I don't see why they can't build the CAN Bus connectivity into Android in a way that it supports the same existing functionality.
I know it's work, money and risk but I think it would be towards a better outcome and there are some potential saving in not rebuilding everything from scratch and maintaining it and paying less royalties etc.