As a general rule, but not always, a bonus is calculated on an interim value which includes the previous bonus. So if the planet was 100CO and you got two bonuses of 5% and 10% it would be calculated as:
newval = 100x1.1x1.05 rather than newval = 100x1.1 + 100x1.05;

As one of the exceptions, the MT provides it's 10% off the base value with no further bonus applied. So the AMC does not stack with the MT bonus, but will stack with PwrGen.

Generally, percentages are a bonus to a base, rather than a slice of a static value. That base is the value to which you have access, not the full rate. Combat is an exception, you start with the full base values of the ship.

As for Q5, AMC does not currently apply to CO. This might be incorrect, I will check with Lee as to whether it should apply to CO as well.