There's the change, and there's what the change says about the project. The change violates the principle that what is in the buffer is there because the user caused it to be there. Since it is a silent change to a principle that vi and its descendants have always followed, it can lead to data loss; the copy in the buffer may have been the only one. The fact that the change was apparently entirely uncontroversial means that neovim does not think through the implications of their changes and/or is not sufficiently concerned about data loss.
If you think the issue is important, you are free to report it; the project has reverted decisions like this when people have complained (most recently, the default value of the `mouse` setting).
On the other hand, considering how much time this had to be discussed, I would think that by and large this is not a mayor concern for users. This commit was made In June 2015, and the discussion about defaults goes as far back as essentially the beginnings of the project in 2014. We inherited this setting from sensible.vim (which many people consider, well, a very sensible minimal configuration), where the issue was discussed and dismissed back in 2013 (https://github.com/tpope/vim-sensible/issues/64). I think the argument there is convincing. Again, if you don't, please discuss it in the appropriate channels.
