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Glad to have both issues raised/flagged for future discussion.  My preference would be to defer the "free will" issue for a bit.  I think it is indeed relevant in the longer term but, as you say, it is a bit bedeviled by problems of definition in its own right (what it means to a compatibilist is different from what it means to a non-compatibilist) and, at least as importantly, there is no direct relation between randomness and free will (one can have the former and not have the latter, even if one is pursuing a non-compatibilist approach). 

The issue of "natural ontological attitudes" (or what I would call "human nature") is, I think, more immediately approachable.  Yes, of course, as both a biologist and a neurobiologist, I think humans are born with "inclinations" that reflect our evolutionary history. 

But I would, as you suggest, avoid the "hard wired" metaphor for several reasons.  One is that, like all organisms, we have quite substantial individual to individual variation in what we are born with; one can speak of averages or norms but doing so misses the fundamental point of variation.   A second is that as a deeply social species, it is incredibly hard to say with any certainty how much of any observed similarities among us reflects genetic as opposed to similarities in experiences for which culture plays a significant role.  A third is that the metaphor itself is flawed; there is no distinction in the nervous system between "hardware" and "software" in the sense that those terms are used with regard to computers.  All parts of the nervous system are simultaneously "hardware" and expressive of "software" in the computer sense.

On top of all this, I would argue that brains in general, and human brains in particular, have been designed by evolution to cope with a continually changing and somewhat unpredictable world.  To put it differently, among the inclinations we are born with is an ability to identify and potentially alter our own inclinations. Given this, I would not only do away with the hardwiring metaphor but with the underlying concept of "natural ontological attitudes."  Yes, there is at any given time a statistically meaningful "human nature," but to describe it is to ignore individual variation as well as the potential/likelihood that it has been different in the past and will be different in the future.