Incorporating @brendan-ward's suggestions.

rasterio/_base.pyx

@@ -377,9 +377,6 @@ cdef class DatasetReader(object):
         """Returns the window corresponding to the world bounding box."""
         ul = self.index(left, top)
         lr = self.index(right, bottom)
-        #if ul[0] < 0 or ul[1] < 0 or lr[0] > self.height or lr[1] > self.width:
-        #    raise ValueError("Bounding box overflows the dataset extents")
-        #else:
         return tuple(zip(ul, lr))
 
     @property

rasterio/rio/merge.py

@@ -87,12 +87,14 @@ def merge(ctx, files, driver, bounds, res):
                 kwargs['height'] = output_height
 
                 dst = rasterio.open(output, 'w', **kwargs)
-                dest = np.zeros((first.count,) + (output_height, output_width),
+                dest = np.zeros((first.count, output_height, output_width),
                         dtype=first.dtypes[0])
                 nodataval = first.nodatavals[0]
 
             if nodataval is not None:
                 dest.fill(nodataval)
+            else:
+                notdataval = 0
 
             for fname in reversed(files):
                 with rasterio.open(fname) as src:
@@ -108,13 +110,13 @@ def merge(ctx, files, driver, bounds, res):
                             masked=True)
                     np.copyto(dest, data,
                         where=np.logical_and(
-                        dest==(nodataval or 0), data.mask==False))
+                        dest==nodataval, data.mask==False))
 
             if dst.mode == 'r+':
                 data = dst.read(masked=True)
                 np.copyto(dest, data,
                     where=np.logical_and(
-                    dest==(nodataval or 0), data.mask==False))
+                    dest==nodataval, data.mask==False))
 
             dst.write(dest)
             dst.close()

tests/test_indexing.py

@@ -17,8 +17,5 @@ def test_window_no_exception():
     with rasterio.open('tests/data/RGB.byte.tif') as src:
         left, bottom, right, top = src.bounds
         left -= 1000.0
-        try:
-            _ = src.window(left, bottom, right, top)
-            assert True
-        except ValueError:
-            assert False
+        assert src.window(left, bottom, right, top) == (
+                (0, src.height), (-3, src.width))

tests/test_read_boundless.py

@@ -13,7 +13,7 @@ def test_read_boundless_natural_extent():
     with rasterio.open('tests/data/RGB.byte.tif') as src:
         data = src.read(boundless=True)
         assert data.shape == (3, src.height, src.width)
-        assert data[0].mean() == src.read(1).mean()
+        assert abs(data[0].mean() - src.read(1).mean()) < 0.0001
         assert data.any()
 
 def test_read_boundless_beyond():