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?
For Computer Science:
1. replace the current academic funding model with pure fellowships. Each individual, from most junior to most senior, gets their own N year funding.
2. Each has a legal entity under which their IP lives and in which the government takes a small, fair, non-voting share.
3. Completely divorce this funding infrastructure from universities -- if someone wants to use part of their grant to pay for PhD courses/advising, great, but make it so that funding science is not contingent on that institutional apparatus.
For lab sciences things are more complicated.
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.)