I should have been more clear. I was using Tim Cook's statement as an analogy for flashing/side-loading. Allowing good guys to do it means bad guys can do it too.
Tricking a user into side-loading malware does not require physical access to the device and is relatively common on the Android side (more so on third-party stores).
Next you'll be saying compilers are backdoors, too. That's not what the term "backdoor" means.
A malicious actor with physical access to your phone
Stop. Physical access means all bets are off.