PBKDF2 in mnemonic algorithms such as BIP39 and Electrum is not meant to provide security, in fact 2048 rounds is an overkill itself. It is as the name suggests a key derivation function, a way to derive more than one key from the same seed phrase.
It's clear that one of the reasons given on BIP39 to allow a password is to make plausible deniability possible:Quote
The described method also provides plausible deniability, because every passphrase generates a valid seed (and thus a deterministic wallet) but only the correct one will make the desired wallet available.
So we are not just talking about a simple account management using different passwords, but an adversarial setting where the password will make some funds inaccessible to an attacker. The greater the number of iterations, the harder the attacker's job.Quote
Safe BIP-39 seed generation with the option for the user to input 12/24 words (complete seed) or 11/23 words (automatically generation of the last word/checksum)
Last word is not the checksum, it contains the checksum. For example in case of a 12-word mnemonic only 4 bits out of the 11 bits of the last word is the checksum. With only having first 11 words, you'll end up with multiple possible words that would satisfy the checksum verification. In other words you can't "automatically" generate the last word.Yes, some bits will be filled randomly so we can "pick" the last word, it's not just a checksum calculation.