No problems with grinding the outer threads on the freehub body because the only thing that uses those threads is the spin-on top cog on Uniglide cassettes. Unless you're planning on using Uniglide cogs any time soon in the future, the threads won't matter to you. Actually, you're only removing 1-2 threads, so it'll still be possible to thread on a Uniglide top-cog if needed.
As to the end of the threads versus inside of the 11t cog, it's not just the shape, but overall length of the spline that matters. Notice that the splines on the HYPERGLIDE-C cassette body that's used with the HYPERGLIDE-C 11t cog is shorter in overall length than the standard Hyperglide body? You can measure the required spline-length yourself by stacking the cogs & spacers upside down by themselves (11t cog on bottom). Then use a depth-gauge on a set of calipers and measure down to the inside of the 11t cog. Compare that measurement with the length of the splines on your existing freehub body and you'll see what the difference is and how much you need to grind off. You need to see some actual NUMBERS for this to make sense. An engineer cannot build a bridge across the river without knowing exactly how wide it is.
I've done this at least 100x, it's pretty simple. You've spent more time typing and asking questions about this than it would actually take to do the procedure.