I would like to achieve a high-availability scenario on two VMs in Azure. I understand and can follow the directions here: https://www.windowsazure.com/en-us/manage/windows/common-tasks/manage-vm-availability/
However, my question is this: are the two VMs supposed to be exact replicas of each other, so that when one goes down, the other takes over? Or does the Availability Set look after this, so that the two VMs can have totally different content and still utilise each others' free resources?
If you're working with Virtual Machines (currently in Preview), then each VM lives in its own VHD. You can make additional instances by creating a VM from an image you build, but at that point, the new VM lives in its own VHD and the actual disk image will then deviate from any other instance as time goes forward. Of course, if each VM is created from the same image, with the same initialization tasks, etc., then they'd have the same software as well. You'd be responsible for upgrading software versions on all the VMs. If you then put these multiple Virtual Machines in an Availability Set, you'd be assured that the Host OS (underlying OS at machine-level) for the VMs you have would not be updated at the same time. You'd also know that different VMs in the Availability Set would be situated in different racks, network segments, etc.
More on Availability Sets: Within an Availability Set, you may have any variety of Virtual Machines - Linux, Windows, different functionality. And... you may define more than one Availability Set.
In the PaaS world, where you set up a Cloud Service with Web and/or Worker roles, those VMs are spawned the exact same way. So adding instances means adding more of the equivalent VMs. If the disk crashed, a new VM would be created just like the others. There are no persistent changes to those OS disks. In the case of Cloud Services, there's fault domains and upgrade domains, which are very similar to availability sets.