Although I'm sure flipper coins can be used for 3-Fly Routines, I'm not aware of any sources that actually teach a 3-Fly with a flipper.
There are plenty of "Coins Across" / "3 Fly" routines utilizing a Flipper Coin. I beleive the main difference between the two are 3 Fly is generally considered to be at the fingertips.
Examination of a flipper coin will show you that it's invention might well have been for an at the fingertips coins across routine. Shells can be used as well. Troy Hooser makes excellent use of shells in his Total Destruction series. He has several 3 Fly versions in the series. Can't recall how many use Flipper vs. shells but he's definately one overlooked coin (and card) worker.