I can't answer for Photomatrix as I have not tried it.

However if you have Photoshop, or similar,  why not get the result you want with that ?

Taking your two exposures and applying a layer mask to the the top layer,  then use the gradient tool to fill the mask with a gradient from black to white.  This achieves the effect of using a soft ND graduated filter. It also has the advantage you can touch in areas of the image to bring the exposure down if you so wish, or create a grad. filter that does not have a straight line.  

Personally I prefer to use the filter on the camera for my own satisfaction of doing it that way. The disadvantage of using software is if the clouds (or anything else) move.

And every one said, 'If we only live,
We too will go to sea in a Sieve,---
To the hills of the Chankly Bore!'
Far and few, far and few, Are the lands where the Jumblies live;
Their heads are green, and their hands are blue, And they went to sea in a Sieve.

Edward Lear
http://www.nonsenselit.org/Lear/ns/jumblies.html