I agree completely, but like to think of it a little differently. While it's easy enough to put your dotfiles on github, and pull them down onto every machine

I agree completely, but like to think of it a little differently. While it's easy enough to put your dotfiles on github, and pull them down onto every machine you touch, or possibly even automate that, it doesn't solve the fundamental problem that software that requires extensive customization is not good software. If the right trade-offs haven't already been made in the default configuration, then it's an immature application waiting for a rewrite.