That was the thing - when they needed the ship to look small, the main model was too big. Magicam had built a one-foot model for TMP, but that went missing and ILM didn't know anything about it, so built the AMT model.
That's why the 2-footer Ent-D was built. However, that backfired since Image G found the 6-footer too cumbersome, so they used the 2-footer during season 2 in situations that should have required the 6-footer (like when the ship flies into the anomaly in Time Squared).
As ugly as I think the 4-footer is, Image G did manage to use the model to create some really good shots of the ship. You can tell how much easier it was for them as the complexity of shots increased.
Most of the new 6-foot shots done by Image G involved the ship moving slowly or standing still. The only time it was used for a complex movement was Booby Trap, I think.