With the high profile of the Timbertex, it will look *almost* like that. It should be sitting down a little lower.
There are three layers to the Timbertex. Two layers of what you see exposed and another layer about 3 inches that is not exposed. That is why that one side is sitting up higher than the other. They did not remove the "nailing" layer from the course under it.
That's pretty much SOP for roofers. I just installed a ridge vent and had to do the same thing where it butted up to the frame/facia. I actually ran it all the way, then cut the last cap in half to cover the very end. As long as you put a good silicone product or roof tar on the nails, they won't leak. Avoid using caulk unless it's got silicone (gets brittle).