It doesn't look like the getCriteria() method picks up relatedTo criteria set by the field name eg.
$query->customFieldHandle(100);
vs
$query->relatedTo([ 'targetElement' => 100, 'field' =>'customFieldHandle' ]);
// $criteria array does NOT contain any relatedTo criteria
$query = Entry::find();
$query->customFieldHandle(100);
$criteria = $query->getCriteria();
// $criteria array does contain the relatedTo criteria
$query = Entry::find();
$query->relatedTo([ 'targetElement' => 100, 'field' =>'customFieldHandle' ]);
$criteria = $query->getCriteria();
Good catch! Just fixed this for the next release.
Craft 3.5.17 is out now with this fix.