KryoFlux - Write what you want!
Well, that's what it says in the readme file, right? We have to start somewhere and this is no shoddy copier that knows about the platform it's working on. It's completely platform agnostic.
Here's a hint that's for free (a "things-to-try-on-a-Sunday-afternoon" hint) but may work for quite some disks: protection in many cases meant a bog standard DOS disk with a key track added. So having said that... Create an ADF and write it back with verify. Key tracks are easy to spot, so only write this one onto the same disk from Stream. You'd be amazed how many disks work when copied this way.
In this scenario all the DOS data will be fine, even if it's not index aligned.