I realize that the post I am responding to is 3 years old. I ran into the thread searching for something completely different but having to do with old 5.25 disks.
You are quite right, those disks had both Atari and C64 formats on the same side. I know this because I did them. For posterity or just plain trivia, here is the story as best as I can remember....
I was a brand new post-doc (nothing to do with EE or programming) and still quite poor. I had known some folks from Mastertronic through a local software company (Microprose) a year or so earlier. In the present cases, the guy who would have to make the flippies was keen on the idea of cutting production time in half - No flipping required..
I knew squat about Atari but was keen on the C64 1541 drives. I had added memory to the one that I had and it allowed you to do some unusual things. As it turned out, I needed that hack to make both formats on the same side. Or maybe it just motivated me to learn how to write whole tracks at particular locations. BTW: Adding memory was from an article that I read somewhere - it was not my creation. Bottom line was that I figured that there was no reason why I couldn't put both formats on the same side.
As I recall, I started with the Atari disk. I can't remember for sure, but I believe that I had to make sure they were on certain tracks only (low ones) and then I would selectively format and place C64 tracks on the diskette (again, this is where the memory expansion on the drive came in handy). There were some rules to follow, but it was pretty straightforward once I had figured it out. It was tested repeatedly and they worked great. They were very happy with it and, again as I recall, they paid me $100 each time I did this. Can't remember for sure, but I think I did this for 5-6 titles, including the two mentioned.
I just saw one of those disks tonight about an hour before reading this thread (I was actually looking for an alignment diskette). From my hand-written notes on the label, it was Speed King and it was dated 9/30/86 and the Atari tracks were on 1-13 and the C64 tracks were on 14-35. I also noted that track 37 was protected. I can't be sure, but I think it was something I came up with and I'm not sure it had anything to do with having both formats on the same drive, and, again as I recall, they didn't want any protection.
Wow, that was 33 years ago! You guys have some pretty good memories.