First, continuous deployment works fine for web projects, but it's not an option if you've got a packaged product that you have to ship at some point. Agile is not a panacea for these environments.

It's important to differentiate between the two kinds of software that you can write. This is post is dead-on for developing truly new software (new features, stuff that fundamentally hasn't existed before, etc). However, estimation (even the kind of project-manager-driven estimation that most engineers, myself included, generally hate) can work really well for software where you're doing basically the same thing you've already done in the past such that the risk of unknown unknowns is extremely low. I've seen it in practice, and when you have a checklist of stuff to do that you've already done with very minor changes in the past that can't be automated for whatever reason (e.g., support a new piece of hardware, except that the new piece of hardware is basically the same as the old piece of hardware with very minor well-documented changes), you can estimate with surprisingly good accuracy.