Note that the FBI got the court order in a hearing to which Apple was not invited. The court gave Apple an opportunity to respond, and it was in the middle of that process when the FBI found another way in.

It's not like the court told Apple "you need to immediately start working on this" and Apple said "no, we refuse".

If the government gets a search warrant and seizes a safe from your home, they don't need the safe-maker's permission to crack it open.

They would if the safe was purely digital, based on vendor-controlled platform DRM that granted the vendor and only the vendor additional access to the safe.