Comment 1 for bug 1651913

Firstly, navigation position (or styles) relies on a class which is added by "siteMessages" function in theme.js. The function counts the number of site messages and adds message-count-{number} class on header element (.header) and main navigation (.main-nav). And this is true for "raw" and core themes.

However in Mahara.org 16.04 upgrade, there where some changes in the templates to make 16.04 look like how it was before as a result I had to changed selectors in mahara-org theme js to get the site message styles to behave correctly. When we updated to 16.10 (current theme), the template especially markups around navigation were changed, there were some consolidations around user navigation and the main navigation is on the page content rather than being below header. The issue you have mentioned above is rather specific to mahara.org theme (I have submitted a patch for that).

As for Mahara core, I can add a note in the documentation about how fixed header with site messages should be styled since there are 3 places (js, markup and css) to consider if one is changed.