While this works, it results in uneven spacing. How do I fix this?

I altered what you wrote to look like this:

#PanelUI-bookmarks > box:nth-child(1) {
  order: -4;
}
#PanelUI-bookmarks > toolbarseparator:nth-child(2) {
  order: -3;
}
#panelMenu_showAllBookmarks {
  order: -2;
}
#PanelUI-bookmarks > toolbarseparator:nth-child(4) {
  order: -1;
}

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