Is your die even accurate to that scale? .0001 is to the ten thousandth of an inch. We're usually measuring to the thousandth, .001. Something I learned in math, just because you can measure something to that degree doesn't mean the process you are measuring is accurate to that degree. What the tolerance is for that I have no idea, you'd have to call them and talk to an engineer.
A lot can cause a ten thousandth variation. Is the die locked down tight? Is there any play in any of the die parts? What about external parts like the shell holder? Did you clean the die and reassemble it to ensure there's no debris or foreign material? Lube can carry shit in there and leave it. Does the brass have a uniform layer of lube? What about the necks, is there more resistance with some vs. others when the expander comes through? Even the amount of force on the over-cam, is it always uniform? Some of this is hard to determine and you just need as uniform of a process as possible. And knowing the tolerances if you're gonna be measuring down to the .0001 or less, to know IF you can measure down to that, is nice.
I'd start with that. You can call the mfg. and ask them what the tolerance is with that particular die too. And kudos for using a micrometer I guess, I'd never have seen that. If it fits the Wilson gauge and it all looks uniform and random cases check out to the .001 I'm fine I suppose.
If you want something that works better than Hornady One Shot (according to a couple of users who did) I make a concentrated lanolin lube you can cut 100% (double it with another bottle of alcohol) and when heated it sprays and spreads with a real even coat and makes working the press easy. Probably the closest thing to Imperial wax that you can spray and certainly the strongest. An easy stroke means less wear on the dies and less work on the brass and can result in a more uniform process in general. Just spray in a bag and mix 'em around or do it in a plastic tub and work 'em around by hand. It's in the PX on here or you can PM me if interested. It won't necessarily be the answer to your prayers with this particular issue but it does help eliminate one variable and makes sizing super easy. You should be able to size with almost no resistance.