With the wide-ranging Compact structure, I would assume BC is quite likely to develop split-party syndrome. When the Apostate is trying to get intel in the local Administratum bureau, any CSMs present would likely worsen his chances. On the other hand side, many combats will see the squishies trying to stay out of the way as best as they can and the meeting with the Khorne berzerkers likely isn't helped by the psyker.
All in all, I foresee many situations in which the most efficient way to tackle the PCs' problems (by the way: is there any specific name for the heretic group? Dark Heresy had a cell of acolytes, DW had a squad,... ) is to split up - and in certain cases, the interplanetary nature of adventures can make those splits last quite some time.
Obviously, a split party means the GM has to divide his attention between players more than usual - and the players in turn receive less screen-time each. How are you going to deal with this situation? Make everyone stay together, no matter how much the group would benefit from acting simultaneously in multiple places? Just let them split up as they wish? Institue some artificial limitation like "no more than 2 active groups at a time"?