I’m not the expert on clamshell mode, but based on what I’ve read about it, I think you’re going there simply because you have an external display and mouse connected.
I suspect (but don’t know) that it won’t happen if you disconnect the mouse. Give it a try. Does the external display remain on when you close the lid with no external input devices connected? Or does it go to sleep?
If you want to put it to sleep without closing the lid, you should be able to do one of:
- Change the Energy Saver/Battery settings to let the Mac sleep when the display sleeps. Then let it wait until the time limit (which you set to an hour in your screen-shot)
- Select Sleep from the Apple menu
- Press the power button and then select sleep from the popup window. (At least I think this still works - it does on my 2011 MacBook Air).
Once it is asleep you should (I assume) be able to close the lid (if you still want to) without waking it up. The only advantage to doing so is dust (as you mentioned) and to prevent a spurious wake-up from something pressing a key (e.g. if you have children or cats).