Currently there is no way to adjust the position of the end cap arrow in Kendo Diagram when the stroke width of the connection is set to a larger number such as 20px.  The end cap protrudes into the shape.  

I've created a simple example, here Dojo Example.

It was also unresolved in the following support ticket:  https://www.telerik.com/account/support-tickets/view-ticket/1418640