Are percentage lengths relative to viewport or viewbox?

Reading Specification 1.1 I get the idea that percentage length values are
defined as relative to the viewport, and viewbox/preserveAspectRatio is
just some handy feature that is mapped to transformation.
But playing with some SVG implementations I found that percentages are
actually relative to viewbox (it become apparent when aspect ratio is
changed by viewbox/preserveAspectRatio) and replacing viewbox attribute
with corresponding transformations doesn't work when percentage lengths are
used in descendant elements.
E.g. in sample
http://www.w3.org/TR/SVG/images/coords/PreserveAspectRatio.svg viewport is
blue rectangle, but rect(0,0,100%,100%) will coincide with red rectangle of
viewbox.
Am I missing some nuance in specification?

Thank you,
Oleg