I think the issue is that the bottom edge of the mountains is too solid and regular. Coming out of the clouds, you'd see the edges of the clouds ON TOP of the bottom edge.

For reference, check out the "small island" on djekspek's Step-by-Step tutorials. Just imagine that those are clouds against the bottom edge instead of forests. The way the mountain and forest/cloud edges interact is right.

One other thing you could try would be having your mountains in one layer, and your clouds in a layer on top of them. Have the mountains go all the way down to the ground, and then cover them up with clouds that are slightly transparent.