News of the quest....
After long delay seeking for inspiration, and coming back upon the work, there is at the moment no way to get out without restructuring the Moodle1 converter implementation :
the Moodle converter process is a simple SAX sequential progressive parsing of the moodle.xml original file, then progressively recomposing a moodle 2 storage backup architecture.
but the core converter did not implement any after_parse() seek back function, so we have in moodle 2 restore plan to make late consolidation processing on restored data. Such a late post processing could solve the course format issue, by post-injecting the course format xml converted sequence into the course/course.xml file.
I'm up to prototype such changes as experimentation, and will provide some results in Moodle Tracker if succeeds...