Propel should add automatically the isCrossRef flag when using the reverse propel-gen command on a valid many to many relationship with cross reference table.
This would be a nice feature to have. I can see how this can set the isCrossRef to true for non-cross-reference-tables in some cases (possibly the reason why this isn't implemented yet), but it certainly is possible. For example, adding an extra flag for the generation, and everytime the schema parser hits a table which is a candidate for a cross-reference table the user has to manually confirm it. This still takes -some- manual effort, but it's still way easier then manually editing the reverse generated schema again and again. Additionally, users who don't need this at all simply don't use the flag, so no one is actually hindered by it.