I think my basic question is .. Word Processor or PDF maker.
And which tool?
I'm struggling to think why you would consider writing in a PDF maker rather than a word processor.
Academia takes a wide range of document formats.
The primary question is which program suits you best for writing. Formatting for upload to Academia is surely a secondary consideration.
I've switched longform writing to Word. Google Docs is another option, as is Libre etc.
Personally, I'd write short academic articles in Tangent Notes because I'd be using the wikilinks as part of the process. Then probably import to Word for formatting and save as PDF. But Academia has many options, and I'd just do this because it fits best with my usual process, and I prefer PDF as a published format. I've a number of PDF editors, some expensive, but would never consider doing the initial writing in any of them.