If “high contrast text” is on in the options, then this indeed will have no effect.
Huh. The log says DXGI_ERROR_DRIVER_INTERNAL_ERROR, which I really don’t know what to do about. But from your explanation it does seem to be a more widespread system issue. 
Correct. The limit is per player.
Their health stays the same. The increase is only for CI4.
Just CI4.
Yes
Medal awarded.
The reason I increased it there is that King of Crabs and also Iron chef had exactly the same health as Egg City, which comes 3 chapters earlier.
Episodes are also randomized, so that successive playthroughs are not exactly the same (e.g. the asteroid locations and speeds will be different). This is an internal change, anyway, don’t worry if it doesn’t make sense.
This is a deliberate choice. The only case where you can’t do this is League dares, and this is due to an internal technical limitation more than anything else.
Shared
This is the only wave (I think) where enemies are generated dynamically in the middle of it, which causes this issue. This also happens with enemies that spawn dynamically (e.g. from saucer wrecks). I’ll investigate, but I don’t think it’s easily fixable.