Part of the enticement for the connection is the fact that, all told, we really know very little about Clarke's Fairy. Remember, what we've seen directly is the domain of Lost-Hope under the reign of the gentleman with the thistledown hair. Given the taking of Christians into Fairy, and the like, there's every possibility that Septimus' family, et al, are present in Clarke's realm.
Granted, Clarke's vision is much closer to the traditional British interpretation, as seen, for example, in the Blue/Yellow/Green/... Books of Fairy, while Gaiman's is much more is typical mythological smattering. Keep in mind, I'm not saying in the least that Clarke has based her realm whole cloth upon the Fairy see in Stardust, but I do see how the two would mesh nicely. It's really quite gratifying to see three (Clarke, Gaiman, Vess) of the foremost authors of contemporary fantasy playing so well together. Now, if we could get Mieville and De Lint into the mix, that'd be a damn fine stew.