The OP on this one has touched upon a major issue that has been present in Revit since day one, and been asked for since by pretty much all users (there are many workarounds for this scenario or that but Adesk has simply not addressed the underlying issue).
This should be addressed as it is an underlying and fundamental issue. We, the designers, architects, engineers, and draftspersons, should be able to control the start and end points of walls, and each of their components... not a program (or a group of programmers, as good as they may be) that doesn't understand just how important it is to show where one layer of sheathing meets another. It matters for fire rated partitions joining non rated partitions, for metal stud walls coming into contact with cmu/brick cavity walls, and many other scenarios. Walls should also respect the end points that we place instead of automatically adjusting them to the wall centerline (this throws off calculations based on length and makes it very annoying when adjusting wall locations and lengths). There simply aren't enough levels of priority to define it all programmatically from within the type, and even if more were added (similar to another Autodesk program that is no longer called BIM, but is anyway) it can be a management nightmare.
The "Wall Joins" command is a joke, and, even if it does manage to run across a solution (after several pushes of the "next", I've even been warned that there were "### possible solutions... procede?" on some complex scenarios) it will often lose that solution upon modifying one of the walls that it addresses.
Just give us an option to turn on grips for individual layers (both in plan and in section/elevation views) and stop adjusting our endpoints, we put them where we did for a reason...
G
Gary J. Orr
(Your Friendly Neighborhood) CADD/BIM/VDC Applications Manager
aka (current and past user names)
GaryOrrMBI (MBI Companies 2014-Present), Gary_J_Orr (GOMO Stuff 2008-Present); OrrG (Forum Studio 2005-2008); Gary J. Orr (LHB Inc 2002-2005); Orr, Gary J. (Gossen Livingston 1997-2002)