If you have two layer, both have 'normal' blend mode but both layer's opacity is 120, than when you merge the two layers, the result is wrong.
If I had 255, 255, 255, 255 pixels on the original layers, the result layer will be:
- its layer blending mode will be correct: normal
- its layer opacity will be correct: 120 (the same as the original ones)
- the pixel will be wrong: 255, 255, 255, 120 - so it gets the opacity of the opacity of the original layer while the new layer gets the same opacity / so as a result, the pixel will be much more transparent.