I think its also missing a named anchor for top that the return to top feature uses... at the moment it returns to top ok with javascript but its missing the actual named anchor somewhere.

It is technically impossible for the template to apply certain landmarks for a module position as it cannot know what module you will be placing there.

This is why in the advanced module options there is the ability to set the correct tag

So with a clean install of 4.0.3 I need to set the Main Menu module to nav and the Login module to aside(?). Then Axe just tells me 'Heading levels should increase by 1'. Is all of this documented somewhere? Do we need a tutorial on how to make a site Aria compliant? Should this issue be closed now or left as a reminder to provide or improve documentation?

Please let it open as a reminder for documentation.

Has this been documented. If so it should be closed as there is nothing to do here

Documentation is still work in progress. But it is not a Joomla issue, that's correct.