You seem to be under the mistaken impression that imagetype "-i0" is a sector image. It is not. It is a flux stream. It is esentially a recoding of the floppy drives data out line. It contains flux transitions, not user data, along with all the "noise" and low level garbage. Flux images must be DECODED to produce a sector image, such as an ADF. Often, flux images can not be written back "as is" and must be processed first. In this case due to lack of index alignment, that is a requirment.
See the manual how to use -i5 (decoded Amiga format) instead. Either to dump the disk directly, or to decode your already dumped flux stream. Note that ADF will not preserve copy protected disks.