Please see my comment to the question. There is no "merge", there is disjunction, conjunction, etc.
Here is my advice. Go step by step in finer detail. For that, don't use combine mode, but perform explicit operations on region objects. Disjunction is done using the
methods, conjunction — via
Also, these operations will make clip redundant. Actually, I advice you to avoid modifying clip region. You can do all your rendering on both shapes and regions:
For transparency, use alpha channel of the fill/outline colors. As simple as that.
There are many other methods to define a shape and render it with color/transparency.