At first glance it sounds like a dopey question. But think about it. Writing in margins has been one of the most useful tools in human history, and for some reason we can't make it happen digitally.
I'm thinking either a browser extension or a standalone electron reader might work well, but only if there are iOS and android apps too. That's a lot of work! And then it's unclear anyone else will be able to read your notes.
Maybe one solution would be to rasterize out a new PDF whenever you draw on it, and just destructively update all your PDFs.
The best solution I've found till now is to just create a text file with the same name as the pdf.
Acrobat searches the PDF body text, layers, form fields, and digital signatures. You can also include bookmarks and comments in the search.
Other PDF applications do it too.