The real advantage of PDF is that the images which are used inside the document are bundled into the same file... Whereas HTML has historically required the image files to be loaded from elsewhere which made it not portable. That said, now with HTML, you can define images with base64 data, so it could in fact replace PDF.
PDFs are treated that way, but it isn't really true. Due to the complexity of the format, there are many PDFs that will display differently in different viewers.
I don't see a problem with giving the document creator the option to go with a fluid or fixed layout and make the software default to fixed layout.
What are some good WYSIWYG vector standards, including the font department? It could be useful for a GUI markup standard also so that we can have platform-neutral GUI's and GUI's over HTTP.
The server side may still have a dynamic/flow layout engine, but calculated coordinates are sent to the client, keeping the client simpler and more predictable.
HTML and CSS theoretically have these properties, but if you asked someone in the publishing industry to layout a book with them they would either quit on the spot or hate you until their dying breath. That or they're a masochist and want to see if they could actually do it because it is theoretically possible.