The changes are already in the upstream (and in the last release of BLIS), so maintaining the source repository is not an issue.
My concern is about ease-of-use for other users. Getting through build docs and manually managing the paths might be a high burden for new users, especially the ones who don't have previous experience with native development. The difficulty of using libraries, in turn, is a big disincentive for library devs to provide an Emscripten port. And without a collection of easy-to-use libraries Emscripten would not get as wide adaption as it deserves.
What I'd like to have is an Emscripten's analog of naclports project (which contains ports of different packages for Native Client technology). It is fine if, at least initially, only open source packages would be accepted, and they would need to rebuild with every toolchain update (this is how naclports currently works). If a package manager would provide a universal way to build and install packages, it would be of great benefit for both Emscripten ecosystem and OSS libraries.
Regards,
Marat