The only thing that it seems to get from the index is the duration of the clip. As a test I renamed index files from other .m2ts files and paired them up using the same file name between the index file and the .m2ts. They all imported correctly except for being cut off prematurely based on the time within the index file.
So if the index says file 00000.m2ts is 2 minutes long but you put a file that is 10 minutes long it will stop the import at 2 minutes and leave the remaining video in the file unconverted. The import for the first 2 minutes is complete and contain no errors so it is using it as a guide.
I don't know what happens when you take a index file that exceeds the length of the m2ts file. I will check that out later.
But, that is it. It looks at the root of the mounted device for the same file structure to find your index and m2ts files, all other files are ignored from what I gather.
I have about 30 hours of video in AVCHD using my Panasonic SD1, its gunna me fun converting that. If I where going to guess it needs the index to build the preview of the clips and then the preview within imovie 08. I am refering to the part that has thumbnails of your video.