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Will you be using the cutout at the drag strip?
If so, it will be just fine. The engine will be at low rpms just for a second, and the rest of the way down the track you'll be at high rpms. For this reason, exhaust velocity at low rpms will not be as important as maximum, unrestricted flow. With the cutout open, the engine will make more power in the higher rpms, right where you want it for drag racing.
If you plan on opening the cutout on the street, or running autocross, where the engine will be in the low rpms a lot of the time, the cutout will decrease low rpm exhaust velocity and therefore decrease low end torque. It will feel like the engine's not as responsive.
I still say get the whole exhaust done, but it's up to you what you do.
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