Greetings,
I am using the twist ties so I have come at this problem from the other direction. I too use the 1/2" ply and homosote. I use a dremel with a cutting bit.
I use a regular twist drill of the same size to drill the basic hole between the glued down ties. Then I place this cutter bit in the hole and move it left/ right to make a slot for the wire instead of a round hole.
You could combine these two ideas if you are making your turnouts in fixtures. Drill your pilot hole as you first stated and then as Ed suggested use a stop to make sure you do not damage the throw bar. A regular drill bit has a point but this cutter bit is flat. You will then have a little slot instead of a hole. With the slot cross ties on either side of the slot are fully supported on the subroadbed. I have also seen holes large enough that the ballast from the next set of ties falls into the hole as does the glue making a mess on the switch machine.
Christopher