Gustavo Maciel provided a link about BlendState, but it did not contain any information about the function of each BlendState option or how to use them. I have had quite a bit of time to play around with XNA now, and I have found the answer to this question through trial and error.
BlendState.Opaque will cause each color channel to overwrite the current render target, rather than alpha blending it in. For the example in my question, I could have created a small texture cleared with new Color(0, 0, 0, 0), and then drawn it onto my terrain layer after beginning the sprite batch as follows:
This could have been done even more efficiently through a .fx file, in a pixel shader, sourcing from a 2D texture with point sampling. Each pixel in the source texture would represent a single tile, and empty pixels would represent "no tile". Tiling this way is considerably easier and more efficient, as only 1 draw call is required to build the entire terrain layer, versus one for each tile if you rebuild every frame. It also prevents you from having to deal with preserving the terrain layer's state if you only update when tiles are actually changed.