Two reasons I can think of:
* Interrupted ninja builds can leave output directory with truncated files (not all steps think to update their outputs atomically)
* Interrupted recipes don't get to perform their clean-up steps (many don't require clean-up steps, but some do)

The idea here would be to write a "in-progress.stamp" file at the start of a recipe, and then delete it at the end of the recipe. If the next recipe runs and finds the file has not been deleted, then it knows something odd is up and should perform a clobber of the output directory.