This creates a conflict of interests though. Is the research legit or has it been "enhanced" to help a business venture the researcher has in the works?

Oh, for sure. But I wasn't even talking about any business ventures (those are rare in astrophysics...) but more about keeping your code under wraps to prevent others from benefiting from your hard work. Especially, when (as I said in another post), code development is not especially beneficial for your career.

Though it's hard to find a situation where people don't have a (short-term) incentive to make their work look good. One can hope it will catch up with them in the long run, but more likely by then they have a new job (and, in academics, tenure) that will never hear about their past shoddy work.

The solution is to make peer reviewed code produced for a paper be considered equivalent to a paper in tenure decisions. And for all papers in peer reviewed journals that do computer analysis to be backed up by peer reviewed, published code.

That makes code development beneficial for your career, gives an incentive to not keep it under wraps, improves quality, and is likely to reduce the number of published incorrect results.

Of course that is a pipe dream at this point, but what's wrong with dreaming?