It's important to understand that the discrepancy you're encountering is not necessarily due to an issue with the 24-word mnemonic seed phrase system, but could be linked to changes in the wallet software itself.
Different wallet versions might generate distinct addresses using the same public key, which doesn't imply that the underlying cryptographic security system - in this case, elliptic curve digital signature algorithm*** (ECDSA)*** - is compromised or not "future-proof".
The issue might lie with the wallet applications, which might not give the option to select the wallet version.
If you're concerned about verifying the balance across all addresses linked to a specific mnemonic, you could attempt to generate all possible wallet types using your public key and then inspect the assets for each of the corresponding addresses.
The phenomenon you describe, where the same mnemonic seed doesn't restore the original wallet, could also be due to changes in wallet software, rather than a fundamental flaw in the mnemonic system itself.