My config in vim and neovim is also identical. I literally downloaded neovim and just copied over my ~/.vimrc to ~/.config/nvim/init.vim and kept rolling.
The config path is different, perhaps that was it? Or maybe an award installation a few years ago. I remember having a few minor issues with pip, due to unfamiliarity with it. Some python version shenanigans as well. These days I can't really imagine any of those being an issue.