Is there a way to dynamically populate game objects via texture maps?

So you want to know the color of the texture, you can use

http://docs.unity3d.com/ScriptReference/Texture2D.GetPixel.html

knowing the position of your squares, you can check for color.

Providing you use a power of 2 texture you can calculate the number of squares in the texture and their colours. You then instantiate the cubes for each square which matches the colour.

If you get a row of pixels just one pixel high you can calculate the number of columns by looping over them and checking when the colour changes. A different colour would mean the start of a new column. This only works for a checker board of course.

Once you have the row count you can calculate the width in pxels of each square by dividing the texture width by the column count. Knowing the size of each square will allow you to step through the textures pixels at offsets which matchthe width and height of your squares. You can check the colour of each one and see if it matches the one you want to instantiate stuff.

     public Texture2D texture;
 
     private int columnCount = 0;
     private Color[] colours = new Color[2];
 
     private void Start(){
 
         if(texture){
 
             // Calculate number of columns and save their individual colours
             Color[] row = texture.GetPixels(0,0,texture.width, 1);
             Color prevPixel = new Color(1000,1000,1000);
 
             // loop through row and figure out how many columns there are
             for (int i = 0; i < row.Length; i++) {
                 
                 // Save each colour
                 if(columnCount == 0){
                     colours[0] = row[i];
                 }
                 else if(columnCount == 1) {
                     colours[1] = row[i];
                 }
                 
                 // Check if same colour as previous pixel. inc rowcount if not
                 if(row[i] != prevPixel){
                     columnCount ++;
                 }
                 
                 // store previous pixel
                 prevPixel = row[i];
             }
 
             // calculate width of column
             int columnWidth = texture.width / columnCount;
 
             // Loop through texture pixels stepping by the column width in X and Y
             // Check the colour of each square
 
             for (int x = 0; x < texture.width; x += columnWidth) {
 
                 for (int y = 0; y < texture.height; y += columnWidth) {
                     if(texture.GetPixel(x, y) == colours[0]){
 
                         // prevent divide by 0 error
                         float cubeX = 0;
                         float cubeY = 0;
 
                         if(x > 0){
                             cubeX = x / columnWidth;
                         }
                         if(y > 0){
                             cubeY = y / columnWidth;
                         }
 
                         Instantiate(GameObject.CreatePrimitive (PrimitiveType.Cube), new Vector3(cubeX, cubeY, 0), Quaternion.identity);
                     }
                     else if(texture.GetPixel(x, y) == colours[1]){
                         // do something with the other colour if you want
                     }
                 }
             }
         }
     }