On my first few Trijams I only strictly counted the time when I was actively coding or making assets, and I still couldn't get down to 3 hours. Between looking up tutorials and design work and trying to plan how to do things, a 3 hour game would take me all day. But I could get it done, so that was the right challenge level for me.
Now I'm more likely to challenge myself by counting more of the little in-between things instead of stopping and starting my clock constantly, because I don't have all day. If I needed all day, the game wouldn't get done. So that's the right challenge for me now.
I hope to some day be at the level where I can make a game in 3 clock hours from start to finish. But the spirit of the time limit is to get a game made, so interpret the details in the way that works for you. And no one minds if a game took longer than 3 hours, it just isn't eligible to win.