Actually explaining this stuff is difficult 'cuz it's one of those things 'ya just kinda gradually automatically do without thinking after a while but especially as I've transitioned to this approach on and off more recently vs 100% duplicating a character folder with just small edits, I figured this could be valuable insight.
So, the first kind of trick of course when creating an alt is not just necessarily strictly going with what's stated for example as a goal in the case especially with comms, but also examining the impact of secondary elements within reason that justify alterations too (biggest example being Roshiyu's cloak, due to the need of adjusting the position of his shoulder as opposed to a simple rotation within the context of composition).
It's in part recognizing that with the forward position of the shoulder, the support for the cloak is gonna fall more within certain parameters of reason. If the forward shift was a fair bit less, not changing the flow could likely be more acceptable but the difference is enough that it might trigger the brain to actually look at that element a bit more critically. Same for flattening/pushing the chest forward particularly in the final alt, as a result of perspective and motion.
Taking this logic in place, you look at these broader elements as things that'll need to change and become candidates to become separate parts, especially to reduce the amount of other elements that have to be accounted for if you're copying and adjusting things to look the same across multiple duplicates of layers. The most efficient solution is to simply cut things apart, draw out the forms underneath to cover for any further change in position, and find a certain minimum amount need for each part to reduce future editing work and also the load on your computer when time comes to paint.
So, once everything is figured out, you find how many elements can afford to state consistent the whole way through and won't need to be altered, and can leave them untouched the rest of the way. After that, you can designate how many things will need redrawing and alteration and give each collective set their own folder of parts. And have something significantly easier to edit piece by piece if a small thing needs an adjustment instead of a big thing. Sometimes things like armor will still get a separate folder even within the base, primarily if there's lots of smaller elements within for the sake of ease of painting lighting/shadows later. But for example with Ink-Eye's arms below, it's a small enough issue to just go with saving layers and time and merging them.
Faces tend to be something I'll still copy and adjust as a whole regardless if it's just an eye or mouth change 'cuz if you wanna be really nuanced about it, broader impacts of small expression changes realistically will end up reflecting in a lot of other subtle ways throughout the head. (i.e. Knowing in proper application, a happy expression/smile will actually bring changes around the eyes, not just brows and mouth, but take it as a case-by-case basis for art's sake)
The biggest additional part of separating these all out is then applying a mix of masks on multiple levels. Usually on both the basic object level, mixed in with general layer hierarchy in terms of the character themselves, and then a broader section based mask for the entire characters' folder when forms interact. (In this piece, Roshiyu's layers, respectively within each "Version" are always under Ink-Eye's associated layers, so the only time broader masks are applied are in instances that his limbs will be visually in front)
That's the essence of how everything gets pulled together for this kind of thing. Below are varying examples illustrating how parts are overlapping heirarchy-wise and with/without masks.
Hopefully this provides some insight on the underlying nuance to the process, haha. I might not be the most clear about explaining things but it's the best I can do. If you ever want to know more on approaches/examples like this for different artworks, or want me to explain why I make a particular decision on an element on any given piece, let me know! I can periodically put together something more like this every now and then, and it's easier to cite a specific case than at random, lol.
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