2. Someone who beelines to an Advanced Military unit first should be able to Potentially be beat by
-someone who gets a lot of low tech units because they beelined a production tech
-someone who gets a lot of low tech units because they built production buildings instead of science buildings
-someone who gets elite low tech units because they built cultural buildings instead of science buildings
That's going to depend on the relative power differences between units, and what combat looks like. Extreme example: Someone with 50 spearmen isn't likely to beat someone with 2 Giant Death Robots in Civ 5. If the relative power differences are too low, advancement becomes a trivial part of the game.
-someone who beelined and built science buildings and has a few even More advanced units (after they hold off your initial wave)
And how do you think they are going to hold off your initial wave if they not only lack military tech, but also an army because they've invested everything in science? With a tech tree, this situation didn't come up because advancing towards science techs usually helped you pick up some military along the way. If the tech web has a science side and a military side, you're not going to pick up much military while going for science.
I agree Bee-lining should have counters. In the past, they've done a horrible job of balancing the counters and almost always their ultimate solution is to make it more difficult to bee-line, either by moving building/unit further down the tech tree, or by increasing the number of tech connections needed to unlock the tech.
With a tech web, neither of those solutions is practical. If the counter strategies you mentioned prove ineffective, it's going to be a big problem.
3. Adjusting the power of science buildings is necessary because of the positive feedback... you spend science to get Science techs that let you get more science
But the positive feedback effect is true of every aspect of the game. You build production buildings to get more production. More production lets you build more production buildings. You build military to expand your empire. Expanding your empire lets you build more military.
The difference is science benefits literally every aspect of your empire and costs you almost nothing. Even if science buildings didn't exist at all, science would still be the most important thing in the game because of this.
Other things, especially military, have benefits as well as costs. You pay a tech penalty, a culture penalty, and a happiness penalty for taking cities. You gain gold and production, but much of that extra gold and production is offsetting the extra gold and production your spending on military instead of everything else.