To avoid ambivalence I usually use a project specific index name for the CR index. So instead of typo3cr I would name the index myproject-cr. Due to the custom analyzer configuration this will fail hard as the analyzer will then be used (due to the nodetype) but doesn't a actually exist in "my" index as it is only configured for typo3cr index. IMHO we need to find a solution that doesn't depend on the index name.