Just downloaded the Google Clock app. The timer works while on Do Not Disturb if the app is listed as an exception. Also you can activate it by voice if you tell it to set a timer and switch the clock app on the voice screen. :)
I have the same issue. Downloading a third party app is a nice workaround, but less than ideal, since I typically set a timer by voice. Usually I can't take off my gloves to click around and set a timer manually.