I think that's actually really natural, and mimics the patters people were in before industrialization.
Even when I was doing corporate work, that's very much how I ended up actually getting things done. Sometimes it takes hours and hours to wrap my head around some API and make the mental connections, at which point I'll just keep coding until I run out of juice (typically the point when I realize I'm just making errors, coding in circles, and resorting to random edits). The annoying thing in the corporate world is that you can't just spend most of the next day in bed, or on a hike. Instead, I'd work extremely hard one day, then slack off and browse the Internet the next two days, and maybe fix some trivial bug for the sake of a logged checkin.
In my current system, I would say my most valuable habits are:
1) Cardio. My goal is to do 15 - 30 minutes of HIIT every morning. In reality, I end up doing it a few time per week. :-) Honestly, nothing gets me energized and motivated like doing consistent cardio. Two weeks of 30 minutes every day? No depression, constant motivation, sex drive, etc. Incidentally, forcing yourself to do this somewhat uncomfortable act regularly is itself a way to develop discipline.
2) Pomodoros. Once you start forcing yourself to work in focused intervals, you start to realize that you don't actually work that much every day, which is rather liberating.
3) Task estimation. I break down tasks by the number of anticipated hours, then check off every Pomodoro (effectively 1/2 hour) next to the task. Ineffective estimation has been both massively demotivating and very eye-opening. My estimation and attention to detail in analysis has improved significantly from forcing myself to do this. It's also easier to force myself "into the mood" for coding when I'm actually reasonably sure that I only have to do 1.5 hours of work, then I can go play.
4) Block all attention drains in my hosts file. HN, Reddit, etc.