Make messages use JLayouts in Isis and Beez3

Based on discussions in https://github.com/joomla/joomla-cms/pull/3389.
I rewrote the messages overrides for our core templates so they use the new JLayout as well.
Also standardised the conditionals a bit between those two overrides. Like changed `(count($msgList) >= 1)` to just `$msgList` which does the same.

### Testing Instructions
Make sure messages are rendered the same before and after PR is applied. There should be no difference.