What is correct when applying for a visa: VFS or Embassy guidelines?

It's not possible to give a definite answer to the general question. Whenever two parties disagree about some fact, either one could be wrong. But it is possible to give some general guidelines.

First, more recent information is more likely to be correct, the reason for which should be obvious. Second, because the country's government makes the rules, information from the country's government is more likely to be correct.

In this case, it appears that the "new portal" opened by France should be trusted on both counts: it is recent, and it is an official government source.

The problem, of course, is (as you found) that the third-party contractor, in this case VFS, can refuse to accept your application, even if they are wrong and you are right. You really have no choice but to comply with their requirements.

In this case, complying did not make your application less strong (and it is hard for me to imagine how a similar situation could make it less strong), so it's not a huge loss for you. Still, you may want to file a complaint through official channels. Ideally, this would bring to the attention of the French government the fact that the contractor is imposing spurious requirements on visa applicants, and should prompt the government to inform the contractor of the correct requirements.

(Some may say that because the government makes the rules, it's not just "more likely to be correct" but guaranteed to be correct. But it's still possible for governments to give incorrect information, for example because of miscommunication, misunderstanding, or inadequately maintained web pages.)