There was an attempt to address pagelayout in issue
MDL-47033 but the problem is much wider than it looked.
Even though this issue is marked as 'Bug', it should go in master branch only since it affects themes.
In order to test the linked issues setup the custom theme (or patch the bootstrapbase) to use visibly different layouts 'course', 'incourse', 'admin', etc. This can be done as simple as this custom CSS:
Now make sure that:
- only main course page is red (view section-per-page is red also)
- pages that are linked from Course navigation are green
- pages that are linked from Coruse administration are yellow
- magenta seems to be used on "My home", "My private files", "My badges", etc.
There may be some exceptions, also white background will mean some other layout