Body Vendor items are handled by an offsite company named Ground Effects
. They have a full robotized factory for the spray liner (insane quality on that spray job...). There is also a Mopar customization shop inside the plant itself. They handle the side step install and other customization options. Typically they don't spend more than 2-4 days in the shop but like all manufacturing ops, one event can cause big backups (like a paint booth robot suddenly deciding on its own to make a two tone truck).
Sometimes it appears that a vehicle get "stuck" or "held" at certain points in the process. This is normal and can happen. When you think of an assembly line, think of it in three phases: Framing, painting, and final assembly. It's actually one line in three parts. Between these lines are hold areas that act as a buffer in case one of the phases gets backed up or slowed for a reason (see paint booth example above). It also allows vehicles to be pulled off the line in case there were issues that can't be taken care of on the line. The vehicle is inspected between these points to ensure the quality is where it needs to be at the end of frame, at the end of paint, and the very last and final inspection.
Sometimes a paint robot will miss an area (due to a pressure drop or other issue), a welding machine misses a weld due to an issue, or some other issue happens. These body shells are pulled off the line, fixed and injected back into the line to continue on to the next phase. If they can't be fixed, panels are pulled and the shell is scrapped (rare but it happens). These points are the only places in the process where vehicles can be rearranged or pulled in the production process. Otherwise, it's considered a "frozen rope" once it hits final assembly.
If you want to see a pretty cool video illustrating the highlights of that process, the "Inside Out" video about the 2015 Chrysler 200 is pretty similar to the process you will find at Warren and Saltillo.