When you mention vinyl spackle, are you talking about silicone caulking? If so, then this is not what you want to finish your edges.
The products mentioned above will both work... Bondo is (usually) used for filling in dents on car bodies. It comes in a pasty form and you mix in the hardening agent. Then you have about 15 minutes to spread it on the area to fill (like frosting a cake), wait for it to dry and then sand sand sand. Spackle is mostly used for filling in holes in drywall, and many have found it works well for wood arcade projects as well. It is also applied like frosting, but it tends to be easier to sand. But it is also not as hard as Bondo when it dries. You could put your fingernail in the dried spackle and make a dent, but not so easily in the Bondo.
Wood putty is used for filling in small nail holes, and I would not recommend it for smoothing the edge of your wood. It is too think to work with like that, and more difficult to sand. The advantage of wood putty is that it is made from wood, and is stainable - not a concern for your project.