Just a few points I have picked up and not sure what you are doing or using.
The Bullet Seating Die - Does it have a seating insert designed for seating VLD Bullets (Secant Ogive) or is it the standard Tangent Ogive type that just maybe allowing the bullet meplat to touch the bottom of the seating stem rather than use the ogive.
You could try using one of these on your Calipres to give you a greater footprint for measuring.
http://brtshooterssupply.com.au/product ... -base.html
Unless you have a specific Wall Thickness Micrometer like one of these you are not going to get accurate measurements of case wall thickness. The blade of a calipre isn't going to give you very accurate readings, especially the further into the case neck you try and measure.
http://brtshooterssupply.com.au/product ... 1inch.html
Measuring bullet diameters you really need to be using a very accurate micrometer and take one measurement on the bearing surface of the bullet then another near the base of the bullet at the pressure ring which should be a greater measurement. I use one of these...
http://brtshooterssupply.com.au/product ... 1inch.html
This is all getting very expensive and really only to be considered if you are doing competition precision target shooting or you have plenty of money and just like getting things as exact as possible.
If you are seating, removing and re-seating a bullet in the same case you are going to reduce neck tension as every time you seat a bullet you are expanding the case neck ever so slightly unless you size the case neck every time and each time you do that you are hardening the case neck ever so slightly hence producing a slight amount of spring back compared to a case that has not been touched.
In my view every new (unfired) case should be full length resized to make sure they are all the same, then have a mandrel run down the case neck to expand evenly all cases and then have the neck sized to try and create an even set of cases. In my case I anneal every case every reload using an induction annealer set to give the best annealing I can achieve.
I have measured hundreds of Lapua cases and using the measuring equipment listed above I'll tell you that they are not all the same dimensions even over the same box batch lot. They all have differences and also hence why I skim turn case necks even if the chamber size doesn't require neck turning. Also, you really don't want to get into measuring neck thickness until the case has been fireformed and even fired at least twice as the neck material is still moving around the neck diameter.
If you want to be playing with getting bullet seating correct with being exact say 0.020" off the lands then you need a better measuring system for CBTO measurements like a dedicated measuring case and the appropriate guage to measure it like...
http://brtshooterssupply.com.au/product ... aight.html
Unless you are shooting precision target competition I wouldn't really worry about your 0.010" difference you are getting as long as your loaded rounds fit your magazine and bullets are off the lands so your setting of 0.020" gives you that safety margin. If you want to chase the best accuracy the you may want to consider single shot loading rounds that are say jammed 0.020" to jumped quite some distance say 0.100" or more then that will tell you where that bullet likes to be seated in your rifle. Who knows, it may be some jump away from the lands.
One thing I see you mentioned that you don't understand is the partial seating of a bullet. That means that you don't seat the bullet all the way into the neck in one go, say 50% then rotate the case/bullet say 90 degrees and seat the rest of the way.
I don't use the type of press you are using. All my precision reloading is done with In-Line Dies and an Arbor Press.
Hope all this helps a little with your reloading.