If there are better ways to do that, I'm open to suggestions.
I guess that there are different approaches to create a dual boot floppy. I remember some kind of magazine floppy (back in the 80s or early 90s) which had a bootblock for both (amiga and PC in that case) on track 0. The rest was in a custom format so that the data (some kind of magazine) could be shared by booth systems.
So there haven't been any directories or filesystems on that floppy. If you inserted them in the running machine (not booting from them) they couldn't be accessed as normal floppies (NDOS on the amiga and read error on the PC).
So it will be almost impossible to get the two floppies you have (which I assume, need a working filesystem to access there files) onto one dual boot floppy!
The important thing is to know that Atari (and PC) have the filesystem descriptors at the first tracks while Amiga has them mostly at the midway of the disk. But Amiga also requires the boot data on the first track.
So you need to map the diskspace accordingly to each system such that each system is seen as already allocated or unavailable space to the other.
With the Amiga boot track you have to mix two different sector formats on the first track so each system only sees what they need for everything to work.
All in all, if you can setup each filesystem accordingly and build suitable tool for generating the first track as KryoFlux raw stream you could write back such a disk.