Background skinning mode doesn't need (or use) endcaps, so we're talking about making a dock based on individual tiles here (i.e.; a single tile bitmap).
That same body tile bitmap is also going to be stretched/squished as needed, depending on icon size, icon reflection size, etc..., so any endcaps tiles will end-up going to the same process as the main tile itself, which makes it ok. It's like if they were holding invisible icons (assuming we are talking about *extended* endcaps here, of course).
Also, endcaps have their own non-stretchable sections. Just tell the software not to stretch horizontally the first or last half of the endcap bitmap.
Too see how endcaps work (both in the main body and in overlays) I suggest you load the Nexus Nx-WaterBath theme.
Something else that might help for this:
The Theme Builder uses a 'temp scrap' folder named '$ThemeBuilder.~TM' inside the normal Themes folder. Whenever you load a theme into it it copies bitmaps and configuration files into this temp folder. When you drop image files into the picture boxes in the UI, it copies those images into this folder too, renaming them appropriately in the process.
Only when you actually 'Save' a theme using the File menu does it go into its own folder.