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[Update: Same In Final 6.0] System UI Tuner Is Alive And Well In Android 6.0 Preview 3, But There's A New Way To Activate It
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Initially, upon flashing the third developer preview of Android 6.0, we thought our beloved System UI Tuner had gone the way of the dodo. Not so - it's still here, it's just a little less obvious how to get it. If you flashed the latest developer preview and didn't wipe your user data (or received it via OTA), you probably didn't even notice anything changed aside from a little gear icon in your settings shortcut in the quick toggle area, and that little icon is key - press and hold it to activate (or deactivate) the system UI tuner, which will then appear at the bottom of the settings app.
You may need developer options enabled, at least initially, for this to work, though I found that with developer options disabled the feature still worked just fine.
The UI tuner allows you to do things like add your battery percentage into the battery bar in the system tray, remove icons from the tray you don't want, and rearrange your various quick settings. In short, it's an awesome feature - one that Google will hopefully keep around for the final release of Android 6.0.
Now that the final Android 6.0 Marshmallow release is out, we can confirm that this new method of accessing the System UI Tuner still works exactly the same as in dev preview 3.