Hmmm ... not so sure ... If you install Magento from scratch with the default template, 3 columns will be placed on the main page:
http://demo.magentocommerce.com/
In any case, if you see a template that has a two-column layout, while the default layout for the .xml directory is 3 columns, this certainly means that the CMS page of the main page has its own layout.
In the backend, see CMS> Pages> Home. Then, on the “Design” tab, you can find that the “Layout” drop-down menu is set to “2 column with [...] bar”. Setting this parameter to “3 columns” will do the trick.
Theoretically: xml layout files are used for the general layout for each area / module of the site (directory, client, check, search ...), but can be overwritten on each page thanks to the custom Layout that you will find on the CMS Pages, Categories and Products
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