There is a problem. If we make it that the Institution's "drop down nav" checkbox always overrides the site's "drop down nav" checkbox, then there is no need to have the site-level checkbox. The site setting will have no effect except on users who are in "No institution", and possibly users who have selected a custom theme.
I think, it makes sense the way it currently is. That is to say, the "drop down nav" checkbox can seen as part of the institution's theme customization, so it only applies if they choose a custom theme.
We could make it less confusing by adding some JS so that the "drop down nav" checkbox is disabled or enabled, depending on whether or not the "site default" theme is selected.
Alternately, if we really want the institution setting to be able to override the setting even for the "site default" theme, then we need to change the checkbox to a menu so that an institution can indicate that they don't want to override the site setting. In other words, it would be a menu with the options "Site default (Yes/No)", "Yes", and "No".
There is a problem. If we make it that the Institution's "drop down nav" checkbox always overrides the site's "drop down nav" checkbox, then there is no need to have the site-level checkbox. The site setting will have no effect except on users who are in "No institution", and possibly users who have selected a custom theme.
I think, it makes sense the way it currently is. That is to say, the "drop down nav" checkbox can seen as part of the institution's theme customization, so it only applies if they choose a custom theme.
We could make it less confusing by adding some JS so that the "drop down nav" checkbox is disabled or enabled, depending on whether or not the "site default" theme is selected.
Alternately, if we really want the institution setting to be able to override the setting even for the "site default" theme, then we need to change the checkbox to a menu so that an institution can indicate that they don't want to override the site setting. In other words, it would be a menu with the options "Site default (Yes/No)", "Yes", and "No".