There is no reason to say that genetic engineering could not have created a very effective protein. We do not know what computing power military biowar labs have access to that could help find powerfully usable proteins.

You are correct that it could be designed, but it would take a level of computing power that I would be surprised at even the CCP having access to, especially when something like that could be put to a lot of other uses.

No, because a) computer models are limited and can generally always be improved, and b) experimenters could very well have chosen to incorporate unlikely mutations just to evaluate whether they might be unexpectedly effective.

Why would they bother. A) You've already credited them with having the computing power. B) We already have the ability to check for these mutations and their effects so we don't really need a computer. (and something akin to your description of genetic algorithms)

No - this makes the unwarranted assumption that the virus could not have been an experiment not meant as a pathogen, but which turned out to be one. What if it was a piece of research into how to attach to human cells, done simply as a first step in analyzing how to make a better virus, and then it escaped and turned out to be bad?

From your wording I'm assuming that you think they are looking to combine parts from various pathogens in the future, and this was a small part of a larger project.

The reasoning for using a known backbone is similar to why we just don't design new proteins, except in this case its orders of magnitude harder. You can't just combine the best bits from HIV, Influenza and Sars and have a viable virus.
To add to that, if I were to design a bio-weapon it would be a no-brained for an already existing pathogen to be the backbone of it.