Remember the calculator is simply calculating the odds of victory or loss based on casualties from weakest to strongest in attack or defense value. meaning it is removing the weakest units first followed by better ones later.
So in your first example the carriers (from the computers perspective) would be the first units to be removed in a hypothetical (a computer generated battle calc. scenario). However, if it were as you described then your opponent would not be taking the carriers first as you could then simply retreat after one round of combat and all the fighters would be lost. Therefore in the scenario you described your odds of victory would actually increase due to the fact that some fighters (at least two initially) would have to be taken as casualties prior to removing a carrier otherwise you could simply retreat after the first round of battle and force your opponent to loose un-landable fighters regardless.
In your second scenario the Transports are considered normal units unless you are playing a game where transports are non-combat units with no combat value at all. In a situation where you are playing with transports that are not combat units then they would be omitted from the battle calculator. So if the defender is being shown as winning, then those survivors would be only the combat units. Transports would be in addition to those numbers. Now if the transports are combat units (meaning they have defense values) then they would be included in the Battle calculator. However, since the Battle calculator would, in this scenario, be accounting for them it would also be removing them first as casualties since they are the weakest units. If your opponent decides to keep them and take other combat units as casualties first, then you are likely to have better odds of either causing more casualties or winning the battle.
At the end of the day the Battle calc. is good for basic odds of victory or defeat and the number of surviving units. It does not take anything else into consideration. You still have to put some thought towards your maneuvers, possible changes in casualty selection by your opponent and also whether you are playing LL (low luck) or Dice.