As I wasn't able to find a way to create a transparent brush for the mindfusion diagrams, I thought this may be helpful for someone struggling to do the same thing.
Here is a code you can use in the code behind to create a transparent brush (in the following example I am setting the brushes for all tables to be transparent).
Here is the magic line:
DiagramView1.Diagram.TableBrush = DiagramView1.Diagram.ScriptHelper.CreateSolidBrush(System.Drawing.Color.Transparent.A, System.Drawing.Color.Transparent.R, System.Drawing.Color.Transparent.G, System.Drawing.Color.Transparent.B);
(it is kind of long but I think you will get the idea - i tought if I assign the Transparent color properties in the brush constructor, it may produce a transparent brush for me).
Note: this is for the code behind, not in JavaScript, but I think there is a way to do the same thing with JavaScript.
I think the System.Drawing.Color.Transparent.A is the field that makes the magic, this field carries the alpha channel value.
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