FDev probably allowed menu log in case something urgent happens when doing combat, otherwise they woudln't have cared about the issue at all and just not create the timer.
I don't really buy that whole "emergency" thing TBH.
If the doorbell's ringing, your dog's throwing up on the carpet or your kid's got their head stuck in the toilet again you're not going to hang around for 15 seconds, waiting for the timer, so you can quit out of the game properly and go and deal with the emergency.
You're either going to just abandon the game immediately and allow your ship to be destroyed or, if you're a bit shady, you're going to switch off your PC to avoid that happening.
In either case, if something is urgent enough that you couldn't high-wake and then quit, it's probably also urgent enough that you're not going to wait for the timer.
To me, it's really only there as a deterrent against people using it specifically for escaping problems.
If those problems don't involve another human being I guess it's nobody else's business.
If the problem involves a hollow blob on the scanner, however, then you've really got an obligation to abide by the "agreement" you made with another person when you decided to get involved in combat.
It's kind of like showing up for a tennis match, going 2 sets down and then attempting to declare the match void because you think you left the bath running.