During the start-up of 6.1 with a jndi connection in Glassfish i see that liferay alters all tables back to innodb.

It took me 4 hours to change the whole database to mysql cluster on last friday and liferay threw me back within 5 minutes

Is it possible to override this innodb check and change process?

try this entering in the portal-ext.properties

schema.run.enabled=false

Just put the desired engine in portal-ext.properties: