Beda told me that it is an EXTRA theme issue that uses a Bootstrap standard. I have to talk to the team at Elegant Themes to see what they say about it.
I just want to clarify here:
EXTRA does NOT use the default Bootstrap Style, and that is exactly the problem.
They use default classes (like container) of Bootstrap but do alter the CSS that comes with it in Bootstrap.
They should not use such class names, as they simply conflict with Bootstrap.
But on the other hand "container" is quite a common HTML element of course.
I am just pointing this out because there is nothing we can do about it unless over-write the Theme's Styles.
To make the Theme compatible a class name like "container unique-identifier-here" should be used and then the CSS should address ONLY the "container unique-identifier-here", and NOT the "container" only.
What you can do here, is either re-apply the Theme's CSS to Toolset CSS, or re-style the whole site using Toolset Layouts, or not use Bootstrap at all.
If you use Bootstrap there is not chance to avoid a container to use the native Bootstrap CSS.
Also, if you alter the native Bootstrap Classes with Custom CSS so to mimic the Theme's CSS you will, there is no way around it, get issues with the rest of Bootstrap.
This Theme is not Bootstrap Compatible.
And there is not much we can do here. If you plan to use Bootstrap, which is needed if you use Layouts, you have to use another Theme or adapt it so strongly that you are faster by using another theme.
It will conflict with ALL things that ship Bootstrap and override the Theme style (like as for example the setting "Toolset should load Bootstrap 3.0" does.)
I apologise that I cannot give any solution for this.
As said, you can add Theme's CSS to Toolset CSS in Toolset > CSS/JS, but that will eventually overwrite native Bootstrap and create Conflicts.
You could ask the Theme Developers if they can use different Class names, but I think they will not do that.
If you style the whole Template with Layouts you can overcome all this but it will require you to rebuild all the Templates with Layouts and to integrate it as well first:
https://toolset.com/documentation/user-guides/layouts-theme-integration/