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I guess the difference is that how the window is created.
Try :lua vim.api.nvim_open_win(0, false, { split = 'left', win = 0 }) and then try again and change true to false. Do you see the difference?
The best is to open a new window, set all the options you want like winwidth, buftype and filetype and then focus it. I guess that snacks does directly focus the window before setting buffer type and file type so focus.nvim triggers already before you can disable it.
In order to reproduce the issue:
Current config, as taken from the docs, works fine with
neo-tree
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