This is isn’t an issue, it’s an intended change to the way that Mendix renders DOM elements and changes to Atlas.
I understand that it’s frustrating, but it’s a necessary change in my opinion. It simplifies the styling framework and vastly improves the accessibility of the rendered HTML.
These are changes were essential for many customers, so i’m pleased to see that they have been added.
I hope others would agree with me.
You will need to convert your theme so beta 3 can work with it. Check here for the details: