Yes, schema_mysql.sql is how it is supposed to be. Not sure how you got some of the settings? I am quite sure they have never been the default...

Best is you backup your DB and try to change the settings. Make sure you give the DB enough memory to do the migrations (either ram or tmpfs). I can not say if the migrations will just work or if you will need to change the defaults prior to the migration. In the latter case the query should error out and give you a hint about what to do. If something goes terribly wrong, you still have the backup 😊