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See mailing list. The spec. should be clear on how the regions are becoming the containing block of the flow element fragments. For example: <div style="flow-into:article;width:50%">...</div> flowing in regionA and regionB with different sizes. The width of the div will be 50% of the regionA width for the fragment that flows in regionA and 50% of the regionB width for the fragment that flows in regionB.
This is covered in http://dev.w3.org/csswg/css3-break/#varying-size-boxes now.