I'd need the hydro counterparts for the fof halos in the Dark runs. I'm aware of the subhalo_matching_to_dark.hdf5 files but these seem to be for the subhalo catalogs. Should I cross-match fof and subhalo catalogs first? Alternatively, can I also cross-match by position (i.e., the question is whether the IC are identical between the baryonic and Dark runs?)
The ICs are indeed identical (more importantly, the IDs of the dark matter particles are identical). So yes you can either cross-match by position (I would restrict to a delta_mass tolerance e.g. < 0.3 dex) and/or by ID.
The catalog you mention is by ID, which in general will be more robust, and also work for satellites.
I would suggest you use it, by simply taking the answer for the central subhalo of each FoF. (To cross-match from the FoF catalog to the subhalo catalog, you need only use GroupFirstSub).