Some variables not listed when creating feature
If that variable is showing up in the Strongarm admin page, then it means that it's already strongarmed - it probably already exists in another Feature. Use the grep command to search for instances of it in your codebase:

grep -irn 'pathauto_entity_available_entity_types' [codebase-dir]

I bet that will turn up an existing Feature that is managing that variable.

You can't export the same variable to more than one Feature. But you can override it with the Features Override module.