Well, this is exactly why PDF was invented and is doing its job so well. To preserve a desired layout and very specific information on how something has to be outputted.
That comes with downsides, yes, but at its core it's just working fine.
edit: Third option would be to render your content as an image, but that comes with its own downsides.
expect I don't feel many programs are working in PDF natively except for Adobe products. It's always just an export target, or you "print to PDF"
So to me it kinda looks like the format is lacking
I also don't know much about it, but I assume it's not easy to generate programmatically. While for instance generating an SVG diagram/image is generally pretty trivial
That comes with downsides, yes, but at its core it's just working fine.
edit: Third option would be to render your content as an image, but that comes with its own downsides.