TCAS, your writeup provides a valuable review from a new (Turret) user's perspective, but from one who is also an experienced reloader.
Here's some observations I have on your experiences to date. I can't tell when / how you are doing the decapping and sizing, but the comments I have do assume you're doing all processes in the Turret.
1. Now that you have the die setup done, I would do it again, and get it fine-tuned to operation. If one starts with the decapping / sizing die and gets it set properly (firm contact, plus 1/4 turn) and locked down, it provides the basis for setting the rest of the dies properly.
2. The powder-through expanding die's base setting (firm contactwith the shell holder, less 1 turn) is just a recommendation; it depends on how much one wants to flare / work their case. I have mine set at - 5/8 or - 3/4, which works well for the (lead) bullets I use--no shaving.
3. As you've discovered (and is intended), the Lee VMD disk sizings provide 'conservative' weights--e.g., they will always be under. However, any change to the charge is cumbersome, and typically not very flexible. Because I use my Turret for load development (and therefore want to vary charge weights by perhaps .2 gr, and occasionally even .1 gr), I installed an adjustable charge bar on my Pro Auto and never looked back. The Charge Bar allows that kind of charge weight tweaking, and it is done with simply a 'small-turn-of-the-vernier-and-weigh' routine.
As you noted, it is important to verify the charge weight--but rather than doing it with the index rod out, one should verify with turret operation the way you will be reloading. In other words, if one uses the index rod for your reloading, check the weight with a full operation of the turret (4 strokes), for the movement of the turret does impact the charge weight--there's more settling of powder into the disk / adj. bar.
4. The FCD die is normally 'bumpy' in its operation--and sometimes more. It varies from a taper crimp die in that it provides the crimp only--unless final sizing is needed; then a sliding carbide sizer works the brass as well--and that depends, I think, on the brass and the bullet being used. On a Lee 4-die setup, the seater-crimper die is set up to do only seating, and the FCD die does the crimping and a final resizing as needed.
A taper crimp die, OTOH, will apply a final sizing regardless of the current seating and crimp on the cartridge--all depending on how you've set up the die. I shifted to the FCD in station four, like you I get a 'bump' at the crimp operation--and, if I was using a lead bullet, some squeeze / resizing as the die slides over the bullet base and the carbide resizer operates. Then, assuming the cartridge was originally / properly resized in station one, the FCD may not contact the brass again.
I used the taper crimp die for years to solve my SA feed problems--but it could squeeze the (lead) bullet more than necessary. With the FCD die, you get the proper crimp--which is easily adjusted, and not part of a combined seating and crimping that necessitates repeat trials--and then get a post-sizing that ensures good chambering as well.
With a taper crimp die, I could never see a noticable change in accuracy that was repeatable. Indeed, if the bullet was out of spec, the crimp amount would change. With the FCD die, I immediated gained a 1/2" or so increase in accuracy, and clean chambering as well.
I suspect the only problem you may have with the Turret is the occasional ratchet failure. If you avoid short-stroking when in the index bar twist, that probably won't happen. You got an extra ratchet with the press, I think. Order up some more to have on hand, and when it fails, count on doing a strip-and-clean and be sure to install the new one correctly.
Do count on a maintenance routine every few hundred rounds to clean and relube. I found that getting rid of the grunge by cleaning up and re-oiling the index rod goes a long way toward smooth operation. Look for other posts here on Turret Tweaking Tips, too.
Jim H.