But are there cases where a backup of the private keys are still recommended?
It should be default backup method because when you have private key, you have actually key to your coins.
When you have 12 words, you have 12 words not private key. Probably it will resolve to private key, but if some software vendor or some person would modify this 12 word algorith to his need's. Then he woould dissapear and you would be using his services. Your coins would be lost, you won't be able to recover private key then by 12 words coz he only knew method to decode them to private key.
Rare case, but possible.
Are you saying for example that if the creator of Electrum, ThomasV stop working on Electrum and completely abandon the project I will not be able to restore my wallets through the seeds ? Sorry but that is not possible, the creator of Electrum have instructed in the programming of Electrum to restore our wallets with only the 12 word seeds. What you are saying is not possible. Because you are saying this wallet software is centralized which is not.
In the rare case a hardware wallet with closed source like Ledger goes away, we can still import their seeds to other wallets supporting their seed format BIP 39,32,38 or 44 depending on the wallet.