I think the internal cannon is going to be on the shoulder somewhere.
We have had a lot good quality pictures of the underside and flanks of the J20, so if the gun was placed anywhere in those regions, someone would have spotted it already. The only area where we had not had any decent resolution pictures are the topside of the J20, and the only place along the topside where you could place a gun is on the shoulders, similar to where the flankers have their guns.
We have seen pictures which suggest a hatched compartment on the right shoulder/cheek for an IFR, but we can barely see any hint of it on the pictures because of the medium resolution and how good the seams are joined. I'm guessing there is a similar compartment with doors, or a sliding hexagon cover, on the other side for the internal gun, probably a little further back to avoid dazzling the pilot when the gun fires.