You're correct, injecting extra time delay between transactions and settlement is one of the reasons why that architecture is more secure. That's a feature of it, not a bug. That is not the only difference: at almost all Bitcoin exchanges, your hot wallet is on your web tier and exposed to the adversary (so successful adversaries have authority to disburse 5% of your deposits), with the matching/settlement separation, a successful adversary still has no authority to disburse any percentage of your deposits. The hot/cold system also doesn't require e.g. intelligent accounting and reconciliation of those accounts, which is a major reason why the financial system actually works.

BTW: Bitcoin isn't a real-time system. The community widely believes it is, but people who actually understand what is happening would say "cough Yeah by 'real-time' we mean 'an hour later' cough."