JCE Developer here :)
One of the issues here is how SP PageBuilder is retrieving content from the editor, using the getContent but with the "format" option set to "raw", eg:
var t = e.getContent({format: "raw"});
This will get the unprocessed html content from the document.body of the editor, which will therefore, depending on the content, included internal system html code that is usually removed when the HTML is processed.
This method used by SP PageBuilder Pro 4 is different to that used in SP PageBuilder Pro 3, which did not used the format:"raw" option, and worked correctly with JCE Pro.
I can provide a temporary fix for this within JCE Pro (which will be inclued in JCE Pro 2.9.37), by forcing the content to be processed if SP PageBuilder is detected, but it would be preferable if the SP PageBuilder developers have a look at this, perhaps by removing the format:"raw" option when calling the getContent function.