You can use Environment.GetSourceBitmapBgra32(), which will give you an IEffectInputBitmap<ColorBgra32>. Then call Lock() to get the IBitmapLock<ColorBgra32>(). Then use AsRegionPtr() to get it as a RegionPtr<ColorBgra32> which you can just index into, e.g. region[x, y]. Then just compare region[x, y].A == 255 to determine if it's opaque.
Note that this works fine for querying the alpha channel, as the alpha channel is invariant with respect to color space (sRGB vs. linear scRGB vs. whatever other color profile they might have on the image!). If you want to query the RGB values, they won't line up with the color space you're using in the GPU effect, and it'll take some extra work to determine the right thing to do. So that's a topic for another time.