What bonuses are you using for the commanders in this scenario? If the commanders in the defending army have self bonuses that increase defense against cavalry, then the more of them that there are, the more points there will be. Because they have less defense against cav than attack points, the effect will of course be smaller.
Also, individual commander bonuses are limited to the point value of the attribute in the whole army. So if your entire army is 5 units, each commander bonus can never be more than 5 units worth of attack or defense or whatever.
I am not sure why you are using such small armies, but it's possible that the attack calculator isn't taking into account the limit to commander bonuses (that they cannot exceed the attribute for the entire army).
Keep in mind that the battle calculator is a player-created tool and may contain some errors. This does not change the way the game mechanics actually work, which are as described.
Also, there is no difference between one army with 5 divisions and 5 armies with one division each, assuming the commanders and the units led by each commander are the same, EXCEPT that the total value of the commander bonus cannot exceed the attribute for the entire army, so that if you have less than 60 units' value of an attribute assigned to a particular commander, the individual self bonus will be different if he is in an army by himself vs. if he is in an army with a division that contains other units as well.
For example, if I have a t2 infantry commander leading t2 infantry, and he has 50 t2 infantry in his division, which is the only division in the army, his maximum heroism bonus, even if heroism is at level 10, will be equivalent to the attack value of 50 t2 infantry. If I had two such armies, then the total commander heroism bonus would be the attack value of 50 infantry attack plus 50 infantry attack, or 100 infantry attack. (You can substitute "defense" for "attack" anywhere in here, it works the same.)
However, if I put those two commanders in an army together still with 50 t2 swords in each division, the total value of the army attack attribute would be equivalent to 100 t2 swords. Each commander would then receive the maximum heroism bonus, which is equivalent to 60 times his attack value (60 t2 infantry in this scenario). The total commander self bonus for the two commanders would thus be equal to 60 plus 60 or 120 t2 infantry attack value.
So in the extremely limited scenario in which you have fewer than 60 of an attribute value worth of troops assigned to a commander, it makes a difference whether the commander is assigned alone to an army or leads a division in an army with other troops. In practice, compared to the sizes of armies usually used, the difference is essentially irrelevant.
This may reflect my own way of learning, but I suggest that you put together some armies and try attacking some NPCs, even if they are very small armies. You will probably learn a lot more through some simple experiments than you will spending a lot of time discovering every anomaly in the battle calculator, which is intended as a tool, not as gospel.