The only way to get an accurate merge utilizing different blend modes is to Edit > Flatten your image. The resulting image will be exactly as you see it on your screen.
The reason a Merge Layer Down may not end up with the same result is because of situations like this:
Top layer (blend mode normal)
Middle layer (blend mode darken)
Bottom Layer (blend mode lighten)
Base Layer (blend mode normal)
If you select the Middle layer and Merge the layer down into the Bottom layer, what would the resulting Bottom layer's blend mode be? There is no good answer for that question which is why after the merge the image can look different from how it looked before the merge.
The only way to be sure the image result is EXACTLY the same as before the merge is to completely flatten the image.
Then why have a Merge Layer Down function? Well, most of the time the merge works just fine. If the destination layer has a blend mode of "normal", the result will be what you expect. So, the function is very useful for combining layers. The limitation, of course, is when the destination layer has a different blend mode. Just keep that in mind in the future.