I think part of this may be a change in the choice of tools one has to draw the pipe networks. I suggest that use of the (Select) parts to draw, i.e. picking each network component to place in the profile view, instead of placing the entire network one has better control.
And the other side is the Strength and Weakness of a true 3d model of ones pipes. Where it is projecting the pipe, is most likely technically correct, if one were to look at an isometric view of the network, however drafting convention dictates otherwise. One may need to resort to 'trickery' and define a label style, that inserts an ellipse and what ever else you would like to see instead of the pipe 3D projects.