Sounds like we're pulling in the same direction re:improving scientific publishing. At the risk of debating an ally, do you mean to imply that preprint servers are "more archival"? I'm guessing you're familiar with CERN/Zenodo; you trust bioArxiv's continued existence more than CERN's? I rate them as similar, arguably with an edge to CERN.
My experience with publishing is that discoverability is a stronger function of advertising and (especially) getting cited than the publication venue. I do agree that bioarxiv and arxiv are nice advertising venues, but there are lots of ways to skin that cat.
I'm actually only familiar with the arXiv, for physics and computer science research. I don't know much about biorxiv or Zenodo, but they both seem much better than a personal website or github page.
The arXiv has overlay sites, such as http://www.arxiv-sanity.com/ or https://scirate.com/ , that improve discoverability over the basic arXiv interface; for example, you can browse all the papers in a given area posted in the last two months, sorted by some proxy for "interest." Of course there is also Google Scholar, and perhaps there are better ways.
My experience with publishing is that discoverability is a stronger function of advertising and (especially) getting cited than the publication venue. I do agree that bioarxiv and arxiv are nice advertising venues, but there are lots of ways to skin that cat.