There are different differences within the examples as presented (which I'm sure aren't exhaustive regarding possible distinctions, but let's stay focused).
1a: We've been accustomed to working together.
1b: We've got used to working together.
1c: We are accustomed to working together.
I've included a third alternative because that's a more common version that most closely matches 1a in implication (working together is what we're used to / expect). 1b could imply we might not even have wanted to work together when we started (but now we've come to tolerate, bear, put up with the situation.
2a: It takes you a long time to get used to it.
2b: It takes you a long time to be accustomed to it.
2c: It takes you a long time to become accustomed to it.
Where 2c replaces non-idiomatic 2b. I can't really see any scope for saying either version could imply anything different to the other. I'm sure 2a would be far more common in relaxed speech, but there's wrong with the slightly more formal 2c.
3a: He got used to finding fault with everything.
3b: He is accustomed to finding fault with everything.
Where 3a implies that he didn't want to keep finding fault(s), but they were there and he couldn't avoid them (perhaps he worked as a Quality Inspector). After a some time, it no longer bothered him that he had to keep finding fault(s).
3b, on the other hand strongly implies that he does want to find fault. Similar to 1a above, in that the implication is he both wants and expects to do so.
4a: I've got used to drinking my liquor neat.
4b: I'm accustomed to drinking my liquor neat.
Unquestionably here, 4a implies that originally you didn't like drinking neat liquor, but you had to do it so often you can now at least tolerate (and even perhaps enjoy) it. Whereas 4b might be a somewhat "imperious" request / command (Give me a glass of neat liquor, because that's what you normally have, and it's what you're expecting now). Or a withering complaint, if you've just been handed a glass of watered-down whisky when you wanted it full strength.
The main difference (apart from the fact that used to is much more common than accustomed to), is that usually, to be / get used to is more closely associated with adapting to a situation (through past exposure), whereas to be accustomed to often implies expecting / wanting some past pattern to be repeated in a current or future situation.
The exact phrasing given by OP is relatively uncommon 1 compared to what I see as the two relevant "idiomatic standard" usages...
1: to close the stable door after the horse has bolted
to have tried to prevent something happening, but to have done so too late to prevent damage being done
...and...
2: That ship has already left port / sailed
that chance is now gone; it is too late
Note that although those two definitions are similar, they're not generally considered "interchangeable". #1 essentially draws attention to the fact that a potential remedial action is no longer appropriate (because the thing it was supposed to prevent has already happened), whereas #2 is about having missed a chance (it's now too late to take advantage of some favourable opportunity).
OP's version looks to me like a "mash-up" of those two idiomatic usages.
1 I searched for the two following text strings in Google Books...
after the horse had bolted (23 hits)
after the horse had left the barn (8 hits)
I think the ratio is even more extreme with Simple Past (the horse has bolted / left), but you have to scroll through several more pages of results to get to the final totals for those, and I suspect Google Books becomes less "accurate" in such situations.
Best Answer
Call the shots makes a loose analogy with various games, such as straight pool, where players "call" their shots. Straight pool is played on a table with six holes and 15 numbered balls. The object of the game is to "shoot" the numbered balls into the holes. Before each "shot", the player must indicate which ball they are attempting to shoot into which hole. If you successfully shoot the ball you called into the hole you called, then you can shoot again. You keep shooting until you miss a shot.
The analogy is rather loose, because in those games, the person who calls the shots is also the person who shoots. When call the shots is used metaphorically, usually the intended meaning is that the person calling the shots is giving orders that other people follow. The person calling the shots is in a position of authority, setting goals and making decisions that other people implement. The analogy makes sense at a gut level, though, because in a game like straight pool, a person who is calling his shots and repeatedly succeeding tends to project a physical posture of authority and control, making the pool balls do exactly as he says.
Watch Paul Newman in this clip from the movie The Hustler and you'll understand the analogy with negotiation in business. After he calls and makes several shots in a row, he says, "This is my table, man. I own it," (0:58) which is a very cocky way of saying that he believes that he is in control and is going to win.
The article you cite cautions against trying too hard to please the customer. If the customer calls the shots, then the customer is like Paul Newman in that film clip, and you are like the pool balls. The extra word added to the cliché, all, suggests very concisely that you should let the customer have some control, but you should also assert your own limits and expertise when appropriate.