It does not abrade after 3000 ft. It abrades during 3000 ft. The freezing temp can be anywhere in the cloud layer, from the bottom to the last hundreds of feet before the top. So you can't count on stacking them. I suppose the idea was to protect just the fairing and thus the spacecraft from St Elmo's Fire damage, because the booster was still subject to the 5000 ft limitation even if the fairing was not a problem. For example, the command destruct receivers are still vulnerable via their antennas, and there is no way to get around that. But not bringing the fairing up to the same "robustness" as the rest of the vehicle is a bad approach.