In newer versions of jsonnet-bundler this is not strictly necessary anymore, the module name has been only a “legacy” import option for the last year (I just checked the version allowing it went out almost to the day exactly a year ago). If there are conflicts the absolute (go import style) full module name must be specified, which might be nice way to move the ecosystem forward anyways.
I don’t think this should stop us from doing this, I don’t feel strongly one way or the other about the directory structure itself though I agree we could be more consistent.