Magento – Difference Between getChildrenCategories() and getChildren()

In Magento you can only have one root category per store.

If you are unfamiliar with Magento's Global->Website->Store->Storeview Scope structure , try reading something like this: Magento Multi Store, Websites and Storeviews Explained or this:How to set multiple websites with multiple store views in Magento

Long story short. In the front-end you cannot have two Root Categories shown simultaneously. Make two Level-1 categories Root->Default and Root->Collections and move the respective subcategories in there.

You have two options: rewrite or observer.

Rewrite:

The rewrite DOM structure for this is a bit tricky because it is a resource model:

<global>
    <models>
        <catalog_resource>
            <rewrite>
                <flat>Your_Module_Model_Resource_Flat</flat><!-- for example -->
            </rewrite>
        </catalog_resource>
    </models>
</global>

Then in the class file for Your_Module_Model_Resource_Flat you would extend from the core flat category resource model and override this method, changing what you need to change.

Observer:

Register an observer in the frontend for the catalog_category_flat_loadnodes_before event in the frontend, which you can see is dispatched just below the code you referenced. In fact it is preceded by a note stating, "Allow extensions to modify select (e.g. add custom category attributes to select)". In your observing method, you will need to manipulate the select object which is passed in; I have untested peudo-y code here:

public function allowExcludedCategories($o)
{
    $select = $o->getSelect();
    $oWhere  = $select->getPart(Varien_Db_Select::WHERE);
    $select->setPart(Varien_Db_Select::WHERE,array_shift($oWhere));
}