I personally haven't got a 060 based card, so I haven't testet it, but yes I strongly belive it should work 
The only thing you have to do is to copy the 68040/68060 libraries to the "System1/Libs" dir inside your project directory. This is the best method since they will then be included in the System1.lzx archive, which in turn means they won't take up so much disk space.
The only thing I can think of that can be a problem is with the UnLZX command. The 040 version of UnLZX will be used on boot disks meant for 040 & 060 based Amigas, and it might be an issue if UnLZX tries to use functions that are present in the 68060.library upon booting (since the library will not yet be available). I have a Apollo 1240 card and UnLZX doesn't seem to require the 68040 library for running, but I'm not sure what the status is with 060 cards.
Anyway, if the disk won't boot on your Amiga, try to copy the library files to the "Amiga911/Libs" dir instead.
BTW. If you try this, please tell me how it went
running the 68060 version of unlzx without the 060 being initialized by the 68060.library I would say would fail. But having a cpu-specific version of unlzx is unnecessary AFAIK, beacsue the 68060 version of unlzx was just an optimised versions for that cpu to provide a bit of a speed up. As the generic 68k version works on the 68060, and as this an emergency disk, I think speed isn't the main priority, and it would save space, if just a generic 68k version of unlzx was included by default.
i should have time on the weekend to try this and see how it goes.
