Regardless of the motivation, cause, mechanism of #2 - #3 is not the appropriate way to handle the problem. Attack is indistinguishable from unintentional corruption. And #3 trains customers to do the wrong thing when they encounter an attack.

The malicious file was signed with the right certificate. So yeah you should ideally be more careful with checksums but there already was a much more robust and secure authentication mechanism and it was defeated.

Yes, these are two orthogonal egregious security problems.