Oddly, my estimations (I haven't used it yet) for Mathhammer show the opposite. Two unskilled ships (with macrocannons) will almost never hurt each-other under RAW. A Sword's 15 armor is guaranteed to ignore the first macrocannon round that hits it (which still requires one to take out the shields prior), and there's a 50% chance it will completely absorb the first two after shields. Assuming you only have one Macrocannon that can fire (not uncommon for transports) you have literally no chance unless you get two additional hits, and don't have a good chance unless you get three (four hits total). This is essentially impossible with a rating 30 crew. (you would need 6 degrees of success)
With Mathhammer, every (after shield) attack has some chance of doing hull damage. This means our single-battery transport only needs 2 hits (1 for the shield, one to impact) to have a chance to do damage. Two transports slugging it out might take all day (literally, given 48 half-hour turns) but at least they can hurt each other.
Otherwise, your summary above is essentially correct - you appear not to have missed anything RAW that would prevent the attack craft from being as powerful as they currently are in your game.
Edited by Quicksilver