The wires are insulated. In the first picture the insulation is the red and green over the wires.
What I think your asking about is the tubing that goes over the wires.
Its there to protect the wires more and to keep them bundled together.
At the ends where they make their connection it will look like what your seeing and it will not cause problems.
If you try to tape all the way to the end, you will end up with the tape not sticking completely, and a gummed up sticky mess of wires attracting dust and other crap.
Best to just leave them as they are.