Renumbering characters during font minimization? I haven’t encountered that, it would break searching and copying.

Anyway, PDFs for example don’t even say whether a line of text is left, center or justified – they usually store the coordinates of the first character and then spacing to each subsequent one unless defined by the font.

And what if the document contains text boxes, or other Word objects? Well, the text is separate from the underlying rectangle (if there is one) and it’s up to the conversion tool to guess if it’s part of the main text layer.

Sorry, it’s really hard to edit PDFs. You might want to use Inkscape for editing the graphical parts. If you also need to edit paragraphs, I suggest recreating the document by pasting them into Word/LibreOffice, and importing any graphical shapes as SVGs (use Inkscape for the conversion, then you can try Word’s “Graphic > Convert to Shapes” feature).

Really, every software that uses PDF should treat it as an export format, hopefully making it clearer that “saving as PDF” is a visually lossless but structurally lossy and messy process.