Magento 2: How to Override gallery.html File from Vendor

you don't have to override the preference and you should not.

You can easily use a Plugin to set the allow_products data before the method is called. You find a nice tutorial about plugins here:

http://alanstorm.com/magento_2_object_manager_plugin_system

To create your Plugin, you first need to add a type to your etc/frontend/di.xml

<type name="Magento\ConfigurableProduct\Block\Product\View\Type\Configurable">
    <plugin name="changeAllowProductsBehaviour" type="Vendor\Module\Model\ConfigurableProduct\Block\Product\View\Type\Configurable\Plugin" sortOrder="10" />
</type>

Then Your Plugin Class should look like this:

<?php
namespace Vendor\Module\Model\ConfigurableProduct\Block\Product\View\Type\Configurable;

class Plugin
{
    /**
     * getAllowProducts
     *
     * @param \Magento\ConfigurableProduct\Block\Product\View\Type\Configurable $subject
     *
     * @return array
     */
    public function beforeGetAllowProducts($subject)
    {
        if (!$subject->hasData('allow_products')) {
            $products = [];
            $allProducts = $subject->getProduct()->getTypeInstance()->getUsedProducts($subject->getProduct(), null);
            foreach ($allProducts as $product) {
                    $products[] = $product;
            }
            $subject->setData('allow_products', $products);
        }

        return [];
    }

}

Be sure to clear cache and also your var/generation dir to have this changes applied

You can try with

app/design/frontend/{Vendor}/{Theme}/web/css/source/lib/_navigation.less

Read more: How to override gallery.css