No, Bruce, the pin part goes through the slot. And there is no need to have the other 3/8th shackle then. The U part of the shackle goes through the last chain link. You are complicating a beautifully simple arrangement if you do what you describe. It would also totally ruin the way the slot works. Burring the threaded end and grinding down the key end is to stop it being able to work itself undone and to stop the key end catching in the roller assembly. The ideal shackle is a gauge larger than your chain, (which you have), and preferably one with longer than standard limbs, so the U is slightly elongated. That helps to lock it in the slot if there is sideways tension. See below..tho I still do use a swivel, because it makes it easier to swing the anchor around if it comes up point outwards, which does sometimes happen. However, I must admit doing away with the swivel then obviates the need for the second shackle, so as so many are anti swivels, I might well one day try that, as you intend to do. Let me know how that works for you Bruce, in terms of coming up right way round or not twisting.
These were taken when trying to demonstrate (to Marin) how it locks in the slot and does not easily slide up and unset the anchor with sideways pull - or anything other than pull from directly above and in line. I must also admit I use a wire twist through the key to lock mine, and have not ground the key end down, but it does once in a while need a kick to get it to deploy if the protruding pin end catches on the roller assembly. Never a significant issue however.