SI + PRETÉRITO PLUSCUAMPERFECTO DE SUBJUNTIVO + FUTURO SIMPLE / CONDICIONAL SIMPLE

Hola Miltcho

We do sometimes use exactly that structure that you're showing. The use of the Pluperfect subjunctive on the si clause is referring to something hypothetical in the future (as opposed to these examples in this lesson that refer to the past) - the effect of this use of the pluperfect subjunctive here is generally to make it sound as if you really think that something is going to happen but there is that tiny chance of not happening for some unexpected reason; funny enough it adds certainty, not uncertainty. So, in this particular sentence you wrote, the nuance would be:

Si el próximo jueves no hubiera llegado el paquete, reclamaremos/reclamaríamos a la oficina de Correos. 

If (for any reason) we end up not receiving the parcel by next Thursday, we'll/ we'd claim it at the post office. 

You can use both the future and the conditional on the second clause.

I hope this clarified it.

Saludos cordiales

Inma