I see it a little differently. Macro work is all about magnification, and usually as much as you can get. That means that you are operating most often at the minimum focusing distance. That will give you 1:1 whether you use the 60/2.8 on a cropper, or the 100/2.8 on FF. The size of the image of the subject falling on the sensor will be the same. The cropper will of course crop it.
There are therefore 3 advantages at least for using the FF/100 combination over the APS-C/60, even though the image size on the sensor is the same at minimum distance and 1:1 magnification:
1) The FF sensor will capture more of the subject
2) The working distance is greater, so
2a) greater DoF
2b) less chance of spooking timid subjects
3) The larger sensor also allows a smaller aperture before diffraction softening sets in (helping DoF even more)
P.S.
Note on 2a. Although the greater distance means greater DoF, the longer focal length means shallower DoF. If that was all there was to it, the 60 would have the greater DoF, but once you take the circle of confusion into account, it is the 100/FF that is favoured. Or so my calculations lead me to believe - I'm very receptive to correction by better informed POTNers.
P.P.S.
OK - on doing a little more reading, it turns out that at macro distances DOF is proportional to the CoC (and dependent on other things, like magnification and aperture), but independent of distance. The FF body, with the larger circle of confusion will have the deeper depth of field. The factor? You guessed it: 1.6 x.