Magento – How to Auto Populate Magento Products ( 50K )

Yes, use this code

$products = Mage::getModel('catalog/product')->getCollection()->addAttributeToFilter('visibility', 4);

It will get you the visible products, since 4 means Catalog and search visibility. You can combine that with this to add stock check

Mage::getSingleton('cataloginventory/stock')->addInStockFilterToCollection($products);

Based on @Flyingmana's answer I did a little digging and come up with a solution. It seams to work for me.
First my solution, then some explanations.
I've created a file called test.php in the root of my magento instance.

<?php
require __DIR__ . '/app/bootstrap.php';
$bootstrap = \Magento\Framework\App\Bootstrap::create(BP, $_SERVER);
/** @var \Magento\Framework\App\Http $app */
$app = $bootstrap->createApplication('TestApp');
$bootstrap->run($app);

Then I created a file called TestApp.php in the same place with this content.

<?php
class TestApp
    extends \Magento\Framework\App\Http
    implements \Magento\Framework\AppInterface {
    public function launch()
    {
        //dirty code goes here. 
        //the example below just prints a class name
        echo get_class($this->_objectManager->create('\Magento\Catalog\Model\Category'));
        //the method must end with this line
        return $this->_response;
    }

    public function catchException(\Magento\Framework\App\Bootstrap $bootstrap, \Exception $exception)
    {
        return false;
    }

}

Now I can just call test.php in the browser and everything that is placed in TestApp::launch() will be executed.

Now, why this works:
The method createApplication from the bootstrap class is the most important part. It creates an instance of an application class. The method createApplication expects an implementation of the \Magento\Framework\AppInterface that contains 2 methods.
So I created my own class in TestApp that implements that interface. I made the method catchException return false always because I don't want my app to handle exceptions. In case something is wrong, just print it on the screen.
Then I implemented the method launch. this one is called by \Magento\Framework\App\Bootstrap::run. This run method does almost the same thing no matter what the application passed as a parameter is.
The only thing that depends on the application is this line:

$response = $application->launch();

This means that calling \Magento\Framework\App\Bootstrap::run will init the Magento env (maybe do some other crazy stuff...I haven't checked everything yet) then calls the launch method from the application.
That's why you need to put all your dirty code inside that method.
Then the \Magento\Framework\App\Bootstrap::run calls $response->sendResponse(); where $response is what the launch method returns.
That's why return $this->_response; is needed. It just returns an empty response.

I made my app class extend \Magento\Framework\App\Http so I will already have request and response parameters (and others), but you can make your class extend nothing. Then you need to copy the constructor from the \Magento\Framework\App\Http class. Maybe add more parameters in the constructor if you need it.