Jeepers Creepers Dharmit, what's not to get?

The 3D model is just graphics, making it look right doesn't make your Caesar model correct.

You should model as a rigid element from the centerline intersection of the header and branch to the branch centerline intersection of the header wall. From that point model the branch as pipe. Each pipe element shown as a cylinder in the 3D graphics with a cylinder length equal to your element length and a cylinder OD equal to the pipe OD and that cylinder is placed on the centerline of your piping. So, when you skew the cylinder as you have and have a node at the branch centerline and header OD, in your graphics part of theat cylinder will be outside the header and part will be inside the header, but the node on the centerline of the element should be at the header wall.

Hopefully you are using more than just Caesar to evaluate this system.