They probably arent cracked, if you have ever tried to fold a piece that has a 90 degree bend in it (like angle iron for example), you would understand. They notch it so it can be bent and the two ends (approximately) meet; they are then held in that position by being tack-welded to the floor pans which reinforces/shores it all up. I just got done re-freshing my pans and tunnel area and I am trying to remember if mine were relieved like I just described...I want to say yes, but now that I have thought about it, no, no they were not, from the factory they are not relieved instead they actually over bend them to where there is a bit of a gap there at the corner there (on mine anyway). If anyone else has previously done the floors or repaired the channel on your truck, I would guess that they corrected this by relieving the corner and making the edges meet the panel flush. I did this with mine at the top of the hump plus I removed much of the brace there in the center to accomodate my NV4500 and installed a 3/4" sq tube sub-frame for floor support and quick drivetrain access.
In short, once you are otherwise done working on your floors, then weld the seam or "crack" and you should be fine. Weld-thru primer is your friend. Best of luck.
John