That aside, there are some many productivity and tooling gains around organizing your project properly, that it is worth history discontinuities.

Also, I've found that the worse the project organization is, the less likely the team is to separate out different fileset changes into different commits to keep a useful history, or make the use of the git history at all outside of looking at a few recent commits or or sometimes looking at the last release. I've heard this as very circular arguments. Can't re-org because we loose history. Can't maintain good history because the project is too disorganized.