So it's the latter: means that the master public key may be intact but the master private key doesn't match the addresses in the wallet file.
I compared the addresses displayed in
images shared by OP and there are a few same addresses.
In very old versions of electrum, it was possible to import a private key into a existing HD wallet.
Maybe, the wallet file has been created using a very old version of electrum and contains imported private keys and the issue is because the imported private keys are not backed up by the seed phrase.
What do you think? Is that possible?