Please update the contractor as below in this file and try
public function __construct(
You need to put some log at the function \Magento\Catalog\Model\Layer\Category\FilterableAttributeList::getList
this is temporary and therefore can be in the vendor folder directly.
The log we want to use is to know what query runs when the layer filters are pulled in the block \Magento\LayeredNavigation\Block\Navigation
put the lines below just above the ...
It does seem the one that is product attribute that is system does not want to be in the layer.
I will look into it now. Having said that, one would think it might be worth creating a new product attribute identical to the no system one and then 'do assign your data to the new attribute and refresh index..'
that should be a quick win, if you want to do this ...