Your example file was not originally created in Inkscape:
<!-- Generator: Adobe Illustrator 9.0, SVG Export Plug-In  -->

It uses a combination of width/height and viewBox to set the dimensions
of all contained elements of the main viewport (Inkscape itself doesn't
create a viewBox attribute itself, but does respect it when rendering):

   width="541.41699pt"
   height="541.41602pt"
   viewBox="0 0 541.417 541.416"

Attaching the same file recreated with Inkscape without using the
viewBox attribute: now the relation between rectangle and visual bbox
dimensions are correct.

> Yes the stroke is definitely 0.01mm

As far as I know, such small stroke widths (basically none, or at least
my eyes would not see a line with the width of a one-hundredth mm
without a magnifier) are rounded up to a minimal width in the dimensions
on the controls bar of the select tool. My example file uses 0.1 mm to
better illustrate the relations between the geometric dimensions of a
shape and the visual bounding box dimensions).

** Attachment added: "512609-Problem-NEW.svg"
   
https://bugs.launchpad.net/inkscape/+bug/512609/+attachment/1942277/+files/512609-Problem-NEW.svg

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https://bugs.launchpad.net/bugs/512609

Title:
  Width and height don't match in Rectangle and Selection tools

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