Surfaces generated with CAT12 include the FreeSurfer registration spheres needed for projecting data and ROIs between subjects.
Scouts on a subject processed with CAT12 v1742:
Project to ICBM152 as the default anatomy:
Project to the same subject processed with FreeSurfer 7.1:
The ROIs might projects as disconnected blobs, because the different brains have different shapes, and there is no one-to-one correspondence between cortex surfaces of different subjects. But overall the shape and coverage is preserved, and it should be OK for source analysis.
A better approach would be to compute your atlases directly at the individual level with CAT (post your question on the SPM mailing list if you are interested).
Note that the Deskian-Killiany scouts should NOT be projected between brains, as they are already available in the subject space for all the subjects processed with CAT and FreeSurfer.