MySQL slow query log to identify queries that scan tables
I find log_queries_not_using_indexes to be useless.  More useful is the queries that take a long time; this will include any queries that do some or all table scans and are slow, but exclude trivial table scans that are fast.

If a table has 5 rows, it does not really matter whether it uses an index or does a table scan -- the speed will be virtually the same.

These start with the most important queries to work on.  I suggest you work on the first 3, then wait for the impact to happen and get new slowlog:

mysqldumpslow -s t   # to sort by most impact first
pt-query-digest


Also, long_query_time=1 is probably a good starting point.

(I keep my ear to the ground; I have not heard of the option you suggest.  You could file a "feature request" with bugs.mysql.com.)

More

The Optimizer sometimes decides that a table scan is likely to be faster than using an index.  This happens when it estimates that more than 20% of the rows will be touched.  (The "20" varies with the phases of the moon.)  This is because of bouncing between the BTree of a secondary index and the data BTree has some cost.