>> With increasing prevalence of documents being processed online, why hasn't it been the case that the HTML5 option appears as prevalent as the PDF option in say research articles?
Many research articles appear in printed journals. If a research publication uses online distribution rather than a printed journal, then perhaps HTML would make more sense.
Traditionally research papers have been distributed as printed magazines and volumes, so PDF has been a common interchange format.
>> I guess a complete phase-out of PDF is not currently possible, but the provision of HTML5 alongside PDF should definitely be possible?
Yes. It in most cases it should be possible, it depends on the use case, target audience, and perhaps the traditions surrounding what is being published.
>> I found some online options to convert Word documents to HTML5 too so it's clearly not technically impossible, is it?
Probably not. It depends on how the documents are originally written and the "expressiveness" of the documents needs. Many research articles are written using TeX or LaTeX (https://en.wikipedia.org/wiki/LaTeX) which, like PDF, was designed for typesetting.
Microsoft Word and most similar modern word processing software will export to both HTML and PDF. Most LaTeX-based systems also support HTML and PDF output. Other word processing and document preparation software may have a range of output and exporting options depending on what it was designed for.
It is more a question of what the target medium (web publishing, printing, ebook formats, etc.) is and what publishing format best fits the document's needs.