Looking at my factory barrel, it is designed so that the first locking position / groove is shallower (in the lengthwise direction) than the second, hopper position. The depth (inwards, towards the bore) is the same in either position.
If you think your bolt is hitting the barrel, the tip of the bolt does slide inside of the barrel, in either position. This is normal. If you look inside the barrel and see uneven wear on the bore then, I'd be concerned that maybe the O.D. of the barrel is not concentric to the I.D. and it's getting exaggerated in one orientation.