Genuine question, not just trying to be contrary: How does the weakness in using 2048 rounds of PBKDF2 make any difference here?
assuming the keys are generated securely, it probably doesn't, but we need to consider how people
actually generate keys. it doesn't make sense to assume everyone uses best practices.
one problem with BIP39 seeds is they can be generated as brain wallets:
Well, the checksum for a 128-bit seed is only 4 bits, so you have a 1 in 16 chance of passing on the first try, and otherwise you can just change a couple of the words until you do. – Nate Eldredge Jun 8 '19 at 4:23
As an illustration, it only took about a minute of random guessing to come up with the valid BIP 39 phrase baby baby baby baby baby baby baby baby baby baby baby zebra. – Nate Eldredge Jun 8 '19 at 4:26
https://bitcoin.stackexchange.com/questions/88237/is-there-a-reason-to-why-bitcoin-core-does-not-implement-bip39If the keys are chosen securely then there is no gain from having a KDF (and no real harm in having a weak one, except for code complexity). If people use it like a brainwallet then given what we know about how users choose "random secrets" then the KDF is seriously inadequate; considering the infrequency of use and the huge attacker advantages (precomputation because brainwallet schemes cannot be effectively salted, and hardware advantages) you'd likely want something that takes several seconds on the best hardware the user has access to.
The secondary point regarding BIP39 phrases having less entropy than Electrum phrases is easily countered by using 24 words instead of 12.
the same can be done with electrum of course.
https://bitcointalk.org/index.php?topic=1989877.msg19823236#msg19823236this point is unimportant either way, but i would say default user behavior is what matters, not best practices. 12 word seeds = the default across most wallets. i suspect very few people would generate a 24 word seed when using ian coleman's site.
anyway, we're going off on a tangent from the original issue---whether BIP39 is necessary re compatibility. i still say no. there is no reason to discourage people from using electrum in this capacity.