What a patch program looks like when it works
Four things separated the stores that came through September well from the ones that didn't, and only one of them is about patching.
Someone can authorise an unscheduled release. Not a committee. One named person who can approve a documented risk at an inconvenient hour, and who understands that "we'll look at it Monday" is itself a decision with a price attached.
The path to production has been used recently. An emergency patch pushed through a deploy process nobody has exercised in four months is how a security fix becomes an outage. Routine Magento maintenance is boring for exactly this reason: it keeps the emergency path warm.
Monitoring is scoped wider than the storefront. In the September incident, a scheduled malware scan ran against one compromised store and reported it clean, because the implant had installed itself one level above the directory the scan was pointed at. A scanner that only looks where you told it to look will only ever tell you what you told it to say.
Credential rotation is a rehearsed procedure, not a research project. After a compromise, Adobe's guidance is to rotate the store's encryption key and everything it protects: admin logins, integration tokens, payment gateway keys, deploy keys. If nobody on your side knows where that list lives, you will be assembling it during an incident, on the day you can least afford to.