Dawnstorm, thank you for that link.
If it weren't for your question, I might never have stumbled across that blog. I'm happy I found it. That post is thorough, doesn't simplify anything but is easy to read, and has a good sense of priorities.
I knew about the Royal Order before, and I still don't think I understand how/why the it overrules the basic requirements when they fit, but the link shows very similar set-ups to mine and explains proper use, so I need to get over it.
I don't really think of the order of adjective as over-ruling anything. Rather, it's a structure in itself that's reflected in punctuation. You wouldn't make a comma between the last adjective and noun, and the other layers of adjectives extend that principle. It's easy to see with compound nouns. "Swimming pool", for example, is nominally two words, but we see it as a compound, as one word with two components. This is why we would never put a comma between an adjective that modifies this "a big swimming pool". That's fairly straightforward, and most people wouldn't even get the idea that the rule might apply here. As you go up the layers, the separation gets less and less intuitive. Most people wouldn't be tempted to put a comma between the adjectives in "my long black hair", but that's no longer quite as obvious.
What this means is that at some point you'll have some people who, left to themselves, would make a comma, while others would leave it out. We'd have variation. But it's the sort of variation that can lead to confusion, because it's deeply rooted in how we think. And because there's confusion, people try to figure out what's going on and make explicit rules (such as the Royal Order of adjectives). These rules half describe what's going on, but they also arbitrate between different mind sets. Because they half describe what's going on, they're not set in stone and there are exceptions that everyone can agree on (the article mentions a couple of exceptions). But as "rules", prescriptions to follow rather than mere regularities in what we do, they are easy to understand and apply.
Now, this applies to pretty much all of language. It applies, for example, to the rules of how to punctuate co-ordination. This rule is easier to understand in its theoretic formulation than the rule about the order of adjectives, and this is why we tend to think the rule is more basic. But we're only talking about theoretic formulation, and the part where this rule is supposed to describe what we actually do may be faulty. It's possible that the rule is really much simpler, but we haven't found the proper formulation yet.
In my mind, this is not a case of one rule over-riding another, it's a case of a hidden, instinctive order: There is no need for a comma in "the big swimming pool", because we instinctively read "swimming pool" as a compound noun. There is no need for a comma in "my long black hair", because "long" and "black" are on different layers of description. Because it's instinctive, this usually only causes problems when there's real world confusion - and these instances are rare.
When we're editing, though, we're not only relying on our intuition. We need to look over our texts with respect to notions such as correctness, and this biases us toward the formulations of the rules, and away from out instinctive language behaviour. Sometimes we find ourselves correcting things that didn't need correcting and we actually introduce a mistake where there wasn't one (google "hypercorrection" if you're interrested). That's because thinking through language and thinking about language are two different things. So when we think about commas and the order of adjective while editing, some of our confusion might stem from the fact that rules have been formulated incompletely, or that language just isn't as logical as we think it should be. That's why it's important to never let go of our intuitions about what sounds good.
So, on to your examples:
1. "Long, elegant fingers" or "Long elegant fingers"? One thing that's interesting here is that the order of adjective seems to violate the order of adjective. In isolation "long" is size, and "elegant" is observation. So according to the rule (as written down in that blog post), we'd expect "elegant long fingers". Interestingly, that order sounds more unnatural to me than what you put down. Is it one of the exceptions, like the "big old ugly purse"?
I personally think that what's going on here is that we reflect cultural beauty standards, and thus we're not using "long" as size, but we're also using it as an observation/opinion. If that's the case, then the comma is correct, and I'm now changing my vote. "Long, elegant fingers", with the comma, is the superior version.
2. "crisp, blue cotton shirt" or "crisp blue cotton shirt". Observation, colour, qualifier --> no comma. That's applying the rule as it is formulated. I intuitively prefer the commaless version, so I have no reason to change your mind. You said that, in your mind, crisp attaches to blue without the comma, but I don't see that. I'd expect "crisp
ly blue cotton shirt" if that were the case. I'm not aware of a compound adjective "crisp blue" (like, say, "dark blue"), and even if there were one, or if you'd feel like coining one, I'd expect "crisp-blue cotton shirt", since compound adjectives in attributive position (i.e. before the verb, not as a stand-alone adjective in the predicate) tend to take hyphens. So, here I'd go pretty unambiguously for "crisp blue cotton shirt".
It's pretty hard to keep both the intuitive mindset and the analytic mindset active in your head, but we need both faculties when editing. Without intuition we risk hypercorrection, but without analysis we're stuck only with our own intuition (and the point of language is to communicate with others).
(I always feel like apologising after such mammoth posts, but I often post them anyway. I'm a bit too theory minded, at times.)