Say I'm vulture capitalist Tom, and I pay a few gajillion dollars to developer Gupta to create a product for me. I would be understandably pissed if Gupta turned around and sold that same product to competitor vc Janet. She didn't pay for that dev work, I did.
2. With respect to R&D, one big difference is that the government doesn't provide seed funding. They provide grants. If the government wanted equity in research labs, they'd have to pay a lot more. You'll see this in practice if you ever have the extreme displeasure of doing non-useless research in academia. Companies that insist on IP ownership/sharing end up paying much higher premiums for university research contracts. Repealing Bayh-Dole would have no effect on the accessibility of actually useful research; universities and companies would privately fund the useful stuff and leave the government to fund the labs of politically-connected/twitter-famous but otherwise totally useless academics.
(To be clear: we're on the same side here with respect to open access publications.)
In regards to your explanation in [2], that sucks - I kinda figured that's how things were but I sorta went around academia rather than through it so it's interesting to hear. Any hot ideas about how it could be fixed?