I really do not understand why they do not separate these into multiple separate wallets
This was a multisig - meaning M out of N signatures from different signing devices were needed to sign a transaction. The attacker infected enough signer devices to go unnoticed and the signers failed to verify what they were signing on air-gapped devices
This is the part that really surprises me given the amount of money involved.
It's a security domain issue. A highly secure system involves highly secure controls. Bypassing those controls for lower risk activities will typically reduce the security of the entire system. You need an entirely independent low or medium risk system.
The software development practices of banks are probably a good example here.