First of all, let’s clarify one thing. Main clauses are not always independent. I’ll share with you a metaphor I sometimes use with my students. You can imagine complex sentences as if they were trees. The root is the deep structure of the sentence, and on the surface (above the ground) we find the main clause (the trunk) and its dependent clauses (the branches). We can consider twigs and leaves as phrases and words, but let’s concentrate on the trunk and the branches. If you cut off the branches, the branchless trunk will most likely look odd, but it will continue to be a living tree, won’t it?
The same usually happens with a main clause when you take out the subordinate clauses. If these are non-restrictive adjectival or some types of adverbial clauses, the main clause will stand alone, but the situation will differ a lot if we sever restrictive relative, noun or other types of adverbial clauses.
The example you gave of Alice going shopping would illustrate the case where the main clause can still look fine without the adverbial clause of reason. The other two cases are rather particular:
In the first sentence, “These changes in your behavior were probably because you were a teenager…,” the choice of the verb “be” is perhaps not the most appropriate one. We could think of other verbs like “occurred” or “took place,” or even use this structure in which what follows the linking verb “be” is indeed a subject complement: “These changes in your behavior were probably due to the fact that you were a teenager / were probably due to your condition as a teenager / were probably due to your being a teenager…”
In the second sentence, the pronoun “it” (which could be replaced with a demonstrative like “this” or “that”) refers to something that was said before. It would be like an inverted cleft sentence. Instead of saying:
- It could be because you’ve arbitrarily chosen to be defeated by your opponent that you’ve lost so easily (cleft sentence),
- You’ve lost so easily. It (the reason for losing so easily) could be because you’ve arbitrarily chosen to be defeated by your opponent.
A similar case can be found with other adverbial clauses, where “be” merely links the previous sentence with the current one:
- I once traveled all around the world. That was when I was very young.
- I supported her as much as I could. And that was even if I didn’t quite agree with her.
At this stage, I want to show you that the two sentences you have presented show an abnormal use of the verb “be”. In the first case, it is not – lexically speaking – the best choice, and in the second one it just links a previous sentence (not provided in the context) with the “because” clause.