It appears to me that enabling the "Structure Pipe Outlines" displays the vertical location that the pipe enters the structure and not the vertical location where the pipe crosses.
Also it appears the "Structure Pipe Outline" only displays if the "crossing pipe" is not drawn in the profile. This is why you do not see an ellipse for the pipes that run parallel to the alignment.
If the crossing pipe is NOT drawn in the Profile View and "parts masking" is enabled, you will see a cateye, however it will be at the vertical location that the crossing pipe enters the structure and NOT at the actual vertical location at the point of crossing. Drawn like this, it will mask the parallel pipes but if you measure vertical clearances, it will not represent the crossing correctly.
If you "draw in profile view" the crossing pipe, and override the style to show the cateye, it appears the profile view interprets it as the 3D pipe is being drawn. Therefore, even if "Structure Pipe Outlines" is enabled, it will not display the cateye at the structure location.
I think the problem is that "parts masking" will mask any part of the 3D pipe that is within the limits of the structure outline, and since the crossing pipes are typically perpendicular, the entire 3D pipe is within those limits and therefore not visible due to the masking.
Only decent work around I could find is having the crossing pipes on a different Network. The masking trims the parallel pipes and the cateye still shows.
The problem is, since the pipes are no longer on the same network, the crossing pipe cannot "connect" to the structure and if you are using dynamic labels, then it will not show all the pipe inverts. It does work well if you are displaying existing networks because we do not post the elevations like we would for a new network.
Where does someone post for "WISHLIST" items?
You could try a label mask as I use to mask the structure where the pipe goes thru the structure wall see page 5 of my paper from AUNZ 2009 that you can download here.
Thanks for the tip charlesjury4386.
I was able to have my pipes all on the same network, but I have unselected the option to drawn them in the Profile View Properties/Pipe Networks tab after adding all of my network to the profile view. This enables the use of dynamic labels with all of the pipe inverts being labeled. I'm using Civil 3D 2012 edition.
Further musings on the problem: If displaying the connected pipes in profile view is enabled in the structure style, and they are not showing up, possibilities include:
1. The pipes aren't connected to the structure. Make sure the pipes are connected in the Structure Properties dialog box.
2. You have drawn in profile view the connected pipes and overriden them to show as ellipses. This will block out the effort of the structure to show the crossing pipes in the structure style. Remove the connected pipes from the profile view if this is the case.
3. Note that the structure and the pipes have to be in the same network to be connected and, therefore, to have any chance of showing up in the profile view.