TWO RELATED QUESTIONS ABOUT LAYOUTS BREAKING

Our existing production site we've been running for about 9 months has the following software:
Adaptavist Theme Builder (3.3.6-conf210) Powered by Atlassian Confluence 3.0.1

The NEW UPGRADE we're testing is running the following:
Adaptavist Theme Builder (4.1.3) Powered by Atlassian Confluence 3.3

I'm trying to understand why the layout wrappers in the new upgrade are missing several wrappers that were integral to the current production layout. 

* 1) For example the *pagebody* and *pagecontent* wrappers are shown to exist on this HTML example page below but they are not present in the new upgrade's layout. Why? Is it a problem with plugins or our use of panels in Layout Manager, or something else? This and or something else is breaking the way styles are working for the new upgrade.

HTML Structure
https://www.adaptavist.com/display/Builder/HTML+Structure+%28Builder+3.x%29

* 2) Why are closing div tags being added automatically after tables? This also is breaking our existing layouts on production and it appears to still be occurring on the upgrade site but mainly with tables created with || pipes and not { td } markup...

I hope I phrased these questions clearly. Any suggestions or help at this point will be greatly appreciated to get the upgrade on production.