I think there's a distinction to be made in regards to how much of an individual's routine is conscious. For example, I try to live religiously by my consciously planned schedule. It's written out on a whiteboard to the side of me right now. But when my discipline fails I fall into a unconscious, unplanned routine of video games, Netflix, and streams. Both are routines, both are comfortable, but the former is productive and challenging whilst the latter is 'killer'.
That's not a routine, that's a bad habit. "Routine is a comfort, comfort is a killer" is just a pompous way of saying "stay hungry" or "stay frosty" or whatever the k00l k1dz are saying these days (I guess six words about routine). Once you realize Dee Snyder said it you cease to see it as profound. If you're on a good psychological and spiritual footing, your unconscious routine is probably great. After all, it could be argued that minimalism and asceticism allow one to focus only on the important stuff because all else has been eliminated. By not having to think about a lot of stuff, you clear your mind and your soul for more important things.
Don't get me wrong, I think the quote as presented is hollow. It's certainly not profound by any stretch. Having thought about it, maybe I'm perceiving things the wrong way around. When I'm playing games or whatever outside of my scheduled downtime, at least once I'll consciously acknowledge that I should be doing something more productive. But the opposite isn't true. I don't sit there thinking "I could be gaming right now" if I overrun my schedule whilst I'm composing or practicing an instrument. And nowadays, I'll rarely fritter away a whole day gaming unless I purposefully give myself the day off. So in that way, the bad habits are actually the conscious behaviours. I guess it's like you say, if you're in a good place psychologically and spiritually, a healthy routine will come naturally to you regardless of whether it's written on a whiteboard or not.