Override MagentoCatalogModelLayer

I want to override the class

MagentoCatalogModelLayer

In my /etc/di.xml

<preference for="MagentoCatalogModelLayer" type="CustomModuleModelLayer" />

Then I did the class

<?php
namespace CustomModuleModel;

class Layer extends MagentoCatalogModelLayer
{
    public function getProductCollection()
    {
        //Logic to modify the $collection data

        return $collection;
    }
}

And also etc/module.xml

<?xml version="1.0"?>
<config xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="urn:magento:framework:Module/etc/module.xsd">
    <module name="Vhl_Catalog" setup_version="1.0.28">
        <sequence>
            <module name="Magento_Catalog"/>
        </sequence>
    </module>
</config>

But this is not working. I know that I can use a plugin before or after getProductCollection but when I apply the filter

$collection->addAttributeToFilter('custom_attribute', ['neq' => 1]);

But the filter is not working as expected. If I change the scope in a custom attribute, the filter take the last saving value (It does not matter what scope) and not the current scope for store