I think it's a little different then you think. I think it's more like.

1. the IT gating advantage is a race trait, so other races using a IT gate do not get it.

2. In the Calculator it gives you 'amount of damage' and the 'chance of the fleet disappearing' from overgating.

3. If the fleet does not disappear then it get's damaged.

4. If the damage is enough then some ships in the fleet are destroyed.

5. It appears that overgating damage is random, in that sometimes you can overgate without damage and sometimes you can loose ships within a fleet and the remaining ships are undamaged.