Sort buffers and tables on disk, MySQL/InnoDB
If you are still seeing on-disk temporary tables with your max_heap_table_size and tmp_table_size set that high, then chances are you have a handful of queries with GROUP BY/ORDER BY (or a complex join) that are not using indexes effectively and are generating an enormous amount of intermediate data or you have TEXT/BLOB columns somewhere.  Since you said you don't have the latter, I'm guessing it's the former.

You have a few options


Find the queries causing the problem.  You can use pt-query-digest to help summarize the slow query log and make it easier to track down which queries are going to disk.
Ignore it.  This represents less than 1% of your queries.  Unless it's causing you an actual problem, don't worry about it.
If you can't ignore it, keep bumping up max_heap_table_size and tmp_table_size until the problem goes away.  I wouldn't recommend this.


Keep in mind that MySQL pushes large temporary tables to disk for good reason.  Eventually, you risk pushing other data out of memory (or worse, running the server out of memory) in order to process a handful of queries with very large data sets.  Those settings are per table, so if you have any level of concurrency, you could get into trouble very quickly.  I run in production with tmp_table_size/max_heap_table_size at 768MB, but I have 140GB of RAM to work with.  Your headroom is much smaller with only 12GB.