I am fairly new to InDesign’s XML so take what I say with a large pinch of salt.
Moving the placement of text frames in the layout will not shift the content in the xml structure. However juggling the some elements within the XML structure using the Structure View will change the order of the XML and MAY affect the placement of content.
This is because InDesign tags not only content but also the objects that contain content, these have special meaning for InDesign. If you look at the XML in the Struture Pane you will see different icons for different 'types' of XML elements. Text frames or threaded text frames (which are treated as one XML element) by default are usually called 'story'.
My experience is that you can shift elements around in the XML structure without moving things in the layout — as long as you avoid moving things at the text element level eg. elements that contain sentences or words. If these are moved elements will change relationship in the page layout.
As an example. You have a 4 page spread in a magazine layout. The main content is in a threaded set of frames. The pages also contain photographs and captions which were imported much later in the design process. At the end of the editing process, you map paragraph and text styles and tag your photographs.
Everywhere text is autotagged the text frame/s will also be tagged with an InDesign XML story element. Wherever there is tagged text it will be enclosed within the story xml element, which you can rename, but it remains a story element. The large threaded story will show up contained within one long story element, your captions which are tagged will show up in different parts of the xml structure in story elements and the photograph details will be in photo or image elements.
You can now manipulate the XML, create a new element and pull all of the tagged elements of 4 page spread into this new element and order the story and other element to the way you want them to appear in the XML output, even placing elements such as images and other 'story' elements within the flow of enclosing story elements all without changing the appearance of the layout. As long as you do not move text elements around, the appearance of the page layout will not change but exported XML will have the same structure you see in the structure pane.
This is my experience, big caevat, I have not had any experience with XML tables in InDesign.
Essentially you manage two separate documents, one is the page layout, the other XML layout. You cannot juggle the page layout to affect the XML structure, you can, within restrictions, juggle the XML around without affecting the page layout.
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