The LCC's manage this Covid doc check very well - the only pax that have to join a check-in queue are those that want to check-in a bag, all HBO pax have their docs checked at the gate as part of the boarding process.
This is an over-generalisation. Where checking of docs takes place depends both on the LCC concerned and on the airport. Second, I would not consider the checking of documents at the gate to be the nirvana that you seem to suggest it is. I have had extremely chaotic boarding experiences on some airlines and delayed departures resulting from document checking at the gate. Personally, I find advance uploading of documents as a sensible idea but, yes, its unreliability is an issue.