Absolute positioning in fragmented flow in general should be defined outside regions spec (css3-fragmentation I would assume).
Whether or not first region is ICB for named flow content (and therefore positioned content is constrained to regions) or not - that deserves a separate decision, which to me seems related to stacking context decision.
My opinion: if stacking context for region is to be made optional (especially to allow matching stacking behavior of columns), constraining of positioning to regions will have to be optional for the same reason.
See also Hyatt's explanation of WebKit's implementation in http://lists.w3.org/Archives/Public/www-style/2012Feb/0357.html
Moved to fragmentation spec. following Paris F2F discussion and Action Item https://www.w3.org/Style/CSS/Tracker/actions/426.