I just think its rather a cheesy exploit. For instance, lets say its the modern era, and I invade civ "x" with 15 transports. Now they have battleships, destroyers, subs and carriers, and I don't want to get my smaller equiv "modern" navy damaged or destroyed.
So I just keep the 12 caravels I build hundreds of yrs ago as sacrificial escorts. As long as the ai doesn't have 13 individual ships at my point of attack, all my 60 troops land, which is the point. The transports are invulnerable, and my "proper" navy is safe back home. Just seems, well a little wrong to me.