Well sure, but that's always a question of what are you trying to defend yourself against(what kind of scenario is the backup helping with). Twin towers are probably good enough for any kind of fire/electrical failure/theft/vandalism, but not for a meteor strike, war or as we've seen - terrorism. It's not that people in your example were stupid and didn't see it - just that most likely they didn't consider those dangers as important to have a backup for(if a war breaks out or a meteor strikes New York you probably have bigger problems).

It's the same here - most of the "human extinction"-scale events really don't touch a base that's 10km under water or under ground. Nuclear war or meteor strike? nope. Earthquakes? There are places safe from that. Solar flares? Nope. Deadly virus? Quarantine everyone arriving like you would with the journey to Mars.

Terrorism remains the main risk, but it would have been the same risk on Mars too.

And most importantly - it teaches us how to run an independent colony deep underground, which is important because despite all the Sci-Fi films showing us otherwise, the base on Mars would really have to be underground because of radiation risk.

So yeah, sure, run an underground base for a few decades then you can just transplant the technology to Mars - don't start with Mars first.