Adobe Reader overlaps close objects. We had a bug report on the PDF exporter due to the dark lines visible in Adobe with transparent objects. It seems Inkscape rounds-off in the other direction, showing background between adjacent objects.
The attached file shows 8 rectangles spaced 100px apart. The left four are 100px wide and high, the right ones are 99.9px wide and high. Export to Pdf and compare with the svg at different zoom levels (the lines come and go as you zoom).