Hola Sky

That's a brilliant question! It's quite tricky to explain the specific nuances but I'll try : )) 

Thanks for displaying your questions like this; it really makes it easier.

For "When is it prefered to use the true passive versus the se refleja form?

If we go straight to your example:  "las piedras habían sido extraídas de rocas que se formaron hace miles de millones de años." - you're right, there are two types of sentences. The first one is using the "conventional" passive with ser + past participle because we can clearly assume here that there is an "agent" who is doing that action of "extracting", even though it's not mentioned; we can see that that action was actively done by someone (people, archeologists, etc) - when there is a clear agent there is a tendency to use the conventional passive. This could easily be using the passive "se" to make it a bit more of a relaxed passive, but if we want to add a touch of "formal register" we'd use ser + past participle. Now, the second action using "se": "que se formaron..." wouldn't work at all with the conventional passive because this is what is called "la voz media" in Spanish - this is quite a tricky concept as this is something in between the active voice and the passive voice. This is to do with the fact that it is an action where there is no clear agent, it is as if the subject is in fact involved somehow in that action. But I am going to refer you to this excellent (in my opinion) explanation of "la voz media" from this teacher. It's all explained in Spanish but he talks really clearly. Have a look here. 

 

For "Also, I know this is a lot at once, but I'm struggling to grasp how the use of the passive with "se" differs from the use of the "ellos" impersonal construction

Again, if we go straight to your very good example to compare: "se construye una casa" or "construyen una casa", having in mind that the intended meaning of this is:

"a house is being built [and we don't really need to emphasise or name who is building it, I mean, we know and it's pretty obvious that it is a construction company but that bit of information is really irrelevant, and because we may not even know the name of the construction company but again, it doesn't matter]"

If this is what we want to convey, then the impersonal sentence with the verb in active in the "they" form is the usual: "Están construyendo una casa". The use of the passives here, both of them: "se construye una casa / se está construyendo una casa / una casa es construida / una casa está siendo construida"  would sound very very unnatural. 

You're right at thinking that it is when the action is meant to be coming from a "person/people" that we use the impersonal sentence in the 3rd person plural:

The very important message here is that you've been robed, not who robbed you.

Someone is ringing the doorbell. So, this is the important bit "someone is ringing, whoever it may be, just go and open the door (not who is actually ringing)"

Who cares about who arranges the sales, what I care about is that there are sales every January (that is my message).

In these kind of scenarios only this structure sounds natural or is even correct.

I hope this shows some light on your "passive forms" learning. 

Un saludo 

Inma