If you are outputting a layout for a reflowable medium like HTML or EPUB, you are not putting glyphs in positions. You are constructing graphical objects and defining their relationships (and how those relationships change based on form factor), and you are permitting the output device to render glyphs and put them in positions.
The web browser also "puts glyphs into positions." Neither HTML nor TeX source specifies positioning in the source format though. The same TeX document can be re-rendered at different page sizes, font sizes etc. Really not sure what fundamental difference you are seeing.
This is why we don't use PDF for web pages.