Layouts do not affect toolbars.
There are two modes a lister toolbar can be in (this is ignoring floating/docked toolbars that exist on their own, not attached to a lister):
[ul][li]Global toolbars: These are the normal kind. If they are turned on in one lister, they are turned on in all listers.
[/li]
[li]Local toolbars: These are only turned on temporarily, in a single window. You can turn them on by running a command (e.g. via a hotkey or via a button on another toolbar). The Toolbar command's LOCAL argument makes this happen. For example:
Toolbar NAME=MyToolbar STATE=right TOGGLE LOCAL
(See the Diff/Merge Toolbar thread for a fuller example.)[/li][/ul]
Note that a local toolbar can be turned on for a single lister, but there is no way to turn off a global toolbar for just one lister. If you turn off a global toolbar in any lister, it will be removed from all of them. So you can add extra temporary toolbars to individual windows but you cannot take away your normal set of toolbars (without closing them everywhere and then re-opening them).
That said, you can toggle global toolbars using the Toolbar command, the same as you can toggle local ones. So you could have a button/hotkey which quickly adds/removes them if you don't mind it affecting every window at once.