As Geoffrey Leech (Leech 2004) puts it, “Past hypothetical meaning and the use of the modals is one of the most difficult areas of English not only for non-native speakers, but also for native speakers” (p. 127).
I have always thought that the oversimplified rules of conditional use, so common in old-style textbooks and no longer used in linguistics, should have been abandoned long ago. Your question is a case in point. Obviously, traditional rules cannot explain such sentences.
It is much better to think of (what is commonly referred to as) conditionals type 2 as unlikely (Huddleston’s remote) and conditionals type 3 as impossible (Huddleston’s doubly remote), without any reference to present, past, or future.
Trying to keep both analyses, Leech 2004 somewhat struggles and argues that “[t]here seems to be a growing tendency, in fact, to associate the Perfect after a secondary modal purely with ‘contrary to fact’ meaning, rather than past time” (p. 128).
He also observes that in such sentences, when modals are followed by perfect auxiliaries (in the main clause), “the past meaning of the Perfect seems to have been lost” and only the ‘contrary to fact’ meaning is applicable.
Mittwoch, Huddleston, and Collins 2002 - more linguistically oriented - offer a much better analysis (see Chapter 8 in The Cambridge Grammar of the English Language). They call such constructions doubly remote (conditional) constructions. They give the following examples:
[48] i. If you had told me you were busy I would have come tomorrow.
ii. If you had come tomorrow you would have seen the carnival.
iii. If your father had been alive today he would have been distraught to see his business disintegrating like this.
They argue that the perfect auxiliaries express modal rather than temporal meaning (p. 754). Huddleston 2002 (Chapter 3 in the same grammar) adds that the difference between remote and doubly remote constructions is "not very tangible," cf. his examples below
[6] i b. If they were alive now they would be horrified.
c. If they had been alive now they would have been horrified.
To conclude, Huddleston also argues that doubly remote constructions are "fairly rare" (p. 150).
To my ear, the PEU examples are both colloquially natural and accurately described, while the Macmillan examples, although colloquial, are somewhat misleadingly described: things that are happening now might be better expressed as things that have just happened or have just been reported. But that's a minor criticism.
All these examples exhibit the same basic use of will to express habitual or characteristic action. In this sense (like all the modals in all their senses) this habitual will employs its tensed forms, and particularly the past-tense form, to express nuances which may have little or nothing to do with tense. Speaking very broadly,
Ordinary unstressed uses usually express simple habit—behavior repeated frequently over a long period of time—and tense has its usual significance of present or past reference:
When he's preoccupied with a problem he will often pace up and down for hours.
When I was a child we would always go to my grandmother's for Thanksgiving dinner.
When will or would is stressed, the sense is somewhat different: the habitual action is represented as perversely deliberate. And the tenses are employed somwhat differently, too. The present-tense form generally signifies that the subject currently makes a habit of the perverse behavior:
She will keep falling in love with the wrong people is rhetorically equivalent to She insists on falling in love with the wrong people.
But the past-tense form, although refers to a past action, does not express repeated action in the past but represents the subject's behavior on a single occasion as characteristically perverse:
You would tell Mary about the party ... Even though I asked you not to tell anybody without checking with me, you just can't control yourself around her.
A: He said it was all Jack's fault.
B: Well, he would say that, wouldn't he. Nothing is ever his fault, oh no!
Best Answer
In this case, I don't think there's any ambiguity because the intent is pretty clear.
The intended meaning here is something like this: in the present, the email is being written by the person who placed the order. In the near future, the email will be read by the person who is supposed to be shipping the order. At that near future time, the writer is confident that the reader will understand that they cannot wait any longer for their order.
It wouldn't be interpreted to mean "you won't understand when you read the email, but at some future point after that I think you will understand" because that doesn't really make sense in the context; there's no event mentioned that would cause this change from not understanding to understanding. Here's an example where there would be:
Here the speaker presents a clear opinion that the listener won't understand now, but that an event (growing up) will occur in the future that will make them understand when they look back on this.
Now, as for your suggestions. Must doesn't say quite the same thing. There's a social nuance to the original phrasing; they aren't confident the reader will understand. But they say they are confident because that makes it harder for the reader to come back and say "You placed your order with us and that's final! You're going to wait however long it takes!" Since they've already approached it as "I'm sure you're compassionate toward our situation and are going to be understanding about this", they've made it harder for the company to turn around and hold them to the order. That's why they used phrasing like that, not because they actually are sure they'll understand.
So the reason must doesn't work is because it's confrontational. It doesn't say "I am confident that when you read this you will understand." It says "I am confident that you are required to understand--you have no choice but to understand." So for one thing that doesn't actually say the same thing... It isn't simply saying that the understanding will happen, it's saying that the understanding is required to happen for some reason. It's compulsory. So the two have different meanings, and the version with must is less likely to elicit the response the writer is looking for, because it's missing that subtle manipulation.
Simply omitting will doesn't quite have the same meaning, but it's close enough that it could be reasonably used in this situation. "As I'm sure you will understand" means "in the near future when you read this, I am confident you will understand." "As I'm sure you understand", without the will, means "I'm sure that you already understand, even as I write this, before you've even read it." So there's the implication that the company already knew they'd taken too long to fill the order before they were contacted; they understand already that their customer cannot wait. But this is a pretty small difference in practice; the meaning that's intended is going to be understood whether you use the will or not.
I think what's most likely to be used in this situation is can rather than will. (I get that the book was trying to give will examples, but I still feel like I should explain this.) The version with will sounds a little formal, and without it you do have that implication that they already understood. So you can take the middle road and use can:
Here can means "As I'm sure you are able to understand, have the capability to understand, are an empathetic person who can sympathize and will understand..." You're complimenting them by assuming they're an understanding person, and assuring them that you think they are definitely able to understand the position you're in and respect it and follow through in the right way. I think this is probably more common than the version with will, and it also has another subtle difference that changes the tone of the conversation a bit.