I wonder if there's a way to add a bookmark in Pantheon Files (same as CTRL+D) using some command in terminal?
The simplest way I can think of is to write the location that you want to bookmark to the bookmarks file, for example:
echo "file:///home/user/location Place" >> ~/.config/gtk-3.0/bookmarks
Of course, replacing the location string
/home/user/location with your desired location and
Place with whatever you want to call the bookmark.