I know people do it. Chad from Steelhead Stalkers does it. Guides on the Clearwater do it a lot as well. Thats why they came up with the jig head with two eyes lets. So you can run the dropper from the jig head.
I dont think you would have to worry about spooking them as much as you think. Because what you're trying to do is run the jig 1-3 feet off the bottum, and are usually above the fish. Now if you ran a yarnie or bait with a puffball, your second presentation would probably be level if not higher then your jig. Therefore you wont have to worry about the line hitting the fish.