Looking back over the Crow’s Nest and Double Agents concepts, I see a point that I overlooked in the book (but was covered in the old "Lenore Exegesis Wiki", which expanded upon her ESTJ Ni under pressure example, using Beebe’s concept), that these analogies referred specifically to when the ego became so one-sided that it lost conscious control over too much of its undifferentiated functional potential, which is what we could see in the wiki.
What I had always clearly picked up was them being “the first we run to when the dominant agenda can’t solve a problem”.
So it's not just about one sidedness, but also the issue of what is meant by onesidedness. The term in that context has a specific meaning: the dominant being relied on to the detriment to the auxiliary!

In the book, the double agents can engage in mutiny, of course, but the point made about the crow’s nests is that they are often used to bypass the auxiliary (i.e. the “first mate”, which is the ego’s best shot at attitudinal balance), when they would actually be of more help with that function. (p.90, 101,111).

This should have figured, because the ego’s goal is to hold on to its dominant perspective, and if it can’t do that, then it will at least hang on to the dominant attitude and brain hemisphere embodied in what we would call “function #8 ”.
I had assumed #8 was the “alternate” to the dominant only, while #7 was the alternate to the auxiliary. But it seems they both are alternates to the dominant. (What basically happened, is that I read “dominant agenda” as “preferred function agenda”: dominant AND auxiliary! But I see now “dominant agenda” refers to the dominant function only).
Then when we get older, we begin turning to the tertiary instead of the crow’s nests, which is opposite hemisphere, but still dominant attitude (and Beebe theory would add “ego-syntonic”).
The tertiary takes on the dominant attitude when it provides immediate instinctual defense for an ego under threat. But if the auxiliary is developed well enough to provide attitudinal balance, the type is less likely to rely on instinctual defenses that merely reinforce the dominant standpoint and would be more open to {function #7 —tertiary in opposite attitude} products when adaptation made them necessary.

Should also be mentioned; another use of “unconscious” I’ve heard, is that when a psychological process matures through consciousness into order, it becomes habitual and dominant, and thus, unconscious again.
This can be confusing, especially in reading Jung, because we are so accustomed to thinking that the dominant is by definition the furthest from “unconsciousness”. But it makes sense, and people have testified to not recognizing their dominant function because it is so “second nature”; especially introverts.
Still, it leaves many type seekers wondering whether a function is unconscious because it's dominant, or because it's shadow.
So now we have another definition of unconscious. An undeveloped function, one that is developed to the point of being habitual, and then any introverted perspective, or the products of iNtuition. (Hence, the INJ is the one who deals the most in the “unconscious”, and hence Ni being the hardest function to understand and explain).

I had been attributing “strong Fi” in a dom. Ti (often picked up in the cognitive process tests) to the Crow’s Nests, but now realizing it is more about a weak auxiliary, and my auxiliary has been rather strong, I have to take another look at this for myself.
I imagine it is at certain times I will get into Ti overdrive, and shut off Ne data, that the brain alternative switch will occur. That’s when the logic of the situation I’m analyzing will run out, and it will become a more internal “personal” issue (especially when I run across something that threatens ego’s position on something), and Se will also figure when locking into some fact to support it. Se isn’t the “alternative” to Ne at that point, but to Ti, though it (along with Fi) is arising because Ne apparently isn’t being paid attention to enough at that point.

Also, helps to know what is really Ti and what is Ne, since they obviously get intertwined as the preferred functions, and N and T can be confused as it is. When I demand things to “make sense”, I have been assuming that was perception; hence Ne, but I’m seeing that it really is a judgment, that something is not matching up with an internal blueprint of impersonal order. (And since this disappointment is a “personal” issue, for me, it can more easily lead to the right brain alternate).