You’re correct with your final paragraph, that “venir de” expresses the conditionnel passé when it’s used in the conditionnel présent (just as it expresses the passé composé when it’s conjugated in the présent).

It’s worth noting that what you refer to as an “educated guess” is actually more associated with the conditionnel than the conditionnel passé, and I’d think about it in those terms (i.e, conditional information) rather than as a guess of any kind. So, the fact that “elle aurait quitté la chambre d’hôtel” is conditional on the veracity of “ce qu’on a découvert.” However, we could also possibly see a newspaper headline reading something like “Selon Donald Trump, il serait le meilleur président de tous les temps.” Here we have the conditionnel présent because the claim is logically expressed in the present, but it’s still conditional upon the accuracy of Mr. Trump’s opinion.

The role of the conditional is even evocative enough that what something is conditional on need not be said. Consider this headline from a satirical article by Le Gorafi:
“La SNCF aurait commandé 2000 rames de TER trop rapides pour son réseau.” It’s implied here without ever being outright stated that the information being presented is conditional upon the accuracy of the (fake) reporter’s sources, but it’s a great way for a newspaper to hedge some.

So, I think it’s helpful to think about this in terms of shifting tenses to the conditional rather than in terms of the role of a particular tense. That is, just as the passé composé shifts to the conditionnel passé when we want to emphasize that it’s an “educated guess,” the présent form of venir de shifts to the conditionnel présent. In both cases, it’s really the conditional that matters, not the conditionnel passé per se.

“venir de + infinitif” must be seen here as a replacement of “avoir + participe passé”. “Venir de” is used here as an “verbe auxilliaire”. Your third sentence is therefore not correct, as you guessed.

“Je viens de faire quelque chose” is therefore very similar with the “passé composé” of the verb “faire”, like “je venais de faire” will be similar to “plus-que-parfait” and, as you mentioned, “je viendrais de faire” is similar to “conditionel passé”. The difference between “j’ai quitté” and “je viens de quitter” is that “je viens de quitter” occurred in a very recent past (like you just missed it).

With regards to your example, the “conditionnel” is used to express a doubt. If you observe that the person does not occupy her room anymore, there is no doubt about that and you should say.

D’après ce qu’on a découvert, elle a quitté la chambre d’hôtel qu’elle
louait.

However, my interpretation is that there is a doubt about the moment when she left (she left, and we think that it was only a short while ago)

D’après ce qu’on a découvert, elle viendrait de quitter la chambre d’hôtel qu’elle
louait.

finally, if you have more doubt about the fact that she left, I would add the conditionnel at the first part (I am not 100% sure about what we’ve found, therefore ther is a doubt that she actually left)

D’après ce qu’on aurait découvert, elle aurait quitté la chambre d’hôtel qu’elle
louait.