Change internal position to use top left of the viewport

[jeromepl]

This is a follow up to #321.

As mentioned by @wabain,
"Internal positioning calculations need to be page-relative to handle scaling across zoom levels. However, currently they're all done based on the public-facing coordinate system, which is page top to viewport centre. This is hard to reason about, so the internal stuff should use the distance from page top left to viewport top left."
"As a workaround for the difficulty of the coordinate system, various internal methods use varying coordinate information. This could/should be made more consistent."