A) If you want a .020” oversized bullet channel in your seater, and a loose stem to boot, be my guest. Forster uses a .0005” oversized bullet channel. Wilson uses a thousandth or two, I don’t remember, but the seater stem itself has less than .0005” between itself and the bore and centers the bullet on its interface with a perfectly aligned stem. By screwing a 6.5mm seater stem into a die meant for a 7mm stem, the only thing aligning the stem is the is the threads, all you have to do to see the problem with that is wiggle your seater stem.
B) yes you can use a false shoulder, but doing so with proper headspace requires a lot more care and measurement than the average reloader wants to go through. I had to do it with my wildcat initially as I was originally using a die situation similar to what you’re describing, and I can tell you that it is an unnecessary pain in this situation.
C) you’re right. The 17.5 degree shoulder of the 6.5-06 means the neck shoulder junction moves about .044” forward of a 30-06, compared to moving forward about .015” necking a .280AI down, however, I hadn’t realized off the top of my head just how far forward of a 30-06 a 280Rem shoulder is. Still minimal.
D) I haven’t checked PTG, but they usually have quite a few variations of anything remotely standard. They almost certainly have a 6.5-06 reamer print that is a perfect fit for a no-turn neck after sizing down Lapua 30-06 brass with a couple different throat lengths, guaranteed to include a throat designed for the 140VLD. Talk to Dave Kiff and he’d set you up with which print they already have that works best depending on which brass and bullet you want to use. While you’d pay special order price, you wouldn’t have to pay custom price. It’s possible that you’d want something slightly different than what they had, and then you could go full custom. On the other hand, it’s unlikely that too many folks have done much necking down a .280AI, you’d almost certainly have to pay for a custom print.