It is most likely the channel under the edge of the roof rack. There is a sealant in the channel that dries and becomes chalky. There is a body seam under the sealant. To remove it, you must scrape it out and clean the channel. I used ordinary roofers sealant from the hardware store. Only fill it to the level of the original sealant, so that the channel will fit back in. I used rubber gloves, and a cut off popcycle stick to level the sealer in the channel. I figured out how deep I wanted it, held the stick at that level, and ran it the length of the channel. If you put tape on both sides to the level you want it, you can keep the sealant from getting on the paint.
The one item you must watch out for is the removal of the screws that hold the rack in place. They thread into a rivnut, and the rivnuts are notorious for spinning in the sheet metal instead of the screw turning in the rivnut. If that happens, you will have to remove the headliner to grasp the rivnut. The rivnuts are a bastard metric size made by GM, and are no longer available. There are some SAE sized rivnuts that are close, but you must use the corresponding screws with them. I did this, and fixed the same leak you have.