1. There isn't as much of a difference here as you think. Contractors do turn around and use components developed in public contracts for other consulting projects. Most commonly with other sovereigns, especially when the original contract was with a city or state, but sometimes at the national level as well.

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.)