From looking at the screenshot and how the PDF is displayed in other PDF viewers I don't think the transparency is wrong - rather the stack order: you can work around the issue by moving the rectangle lower in z-order in Inkscape so that the text is rendered above it.
From looking at the screenshot and how the PDF is displayed in other PDF viewers I don't think the transparency is wrong - rather the stack order: you can work around the issue by moving the rectangle lower in z-order in Inkscape so that the text is rendered above it.