This is a bad idea masquerading as a good idea. Before making a pull request (or doing any sort of merge), you should rebase against upstream master (or whatever you're going to push to). However, keeping distinct atomic commits that change one and only one small thing, when possible, is much preferable if bisect or blame is used. If you have broken or poorly written commits, use fixup, reword, squash, etc. in rebase…
This is GitHub's attempt to solve the problem without really changing anything. It won't really change anything. Since pull requests routinely contain a mixture of both changes that should be squashed (fixups) and changes that should not be squashed (independent changes), this just means that you get to pick your poison.