When you mentioned the part about how the "least likely to survive" guy becomes the new captain-owner of the big, powerful ship, it came to me in a flash!
Tuf Voyaging, a collection of shorter pieces about protagonist Haviland Tuf. Some of them had previously been published separately in magazines, then the author decided to add some new material and splice it all together into one book. These stories were written by George R.R. Martin, long before anyone had ever heard of A Game of Thrones and its sequels.
As you say, Haviland Tuf is part of a boarding party who enter this huge derelict "seedship" (called Ark) in the early pages of the book, and he is the only one who survives to become its new lord and master by default. The seedship has all sorts of superadvanced biotechnology, including the ability to clone various animals, or mass-produce certain viruses, etc., which makes it easy (in later stories, after he gets the hang of things) for him to tell the computers to tinker with one lifeform or another to provide a tailor-made solution to an ecological problem on whatever world he is currently orbiting.
Tuf tries to honor his bargains if his clients will hold up their end of the deal (which is not always the case), but sometimes his solutions turn out to have side effects which are not exactly what the local government, and/or the common people, really wanted. This allows Martin to explore some interesting ethical questions.
I don't have my copy handy, so this isn't a precise quote, but I remember that, at one point, a woman who dislikes his drastic solution to a problem then asks him something along these lines: "Who elected you to play god?"
Tuf says drily: "Politicians are elected. Gods normally arise by other means."
