Why is the automatic cheaper than the manual?

The discount you're mentioning likely refers to the fact that the discounts on the T-Cross AT are bigger than those on the T-Cross MT. This is quite normal because dealers rarely order manual transmission models, especially for models like the T-Cross. It's unlikely they'll order manual versions and have them sitting in inventory. Most are automatic models, and dealers aim for quick turnover. Therefore, the discount on automatics is inevitably bigger than on manuals. If you order a manual, the production cycle is longer, and the cash flow back to the dealership is slower, so the discounts are much less compared to automatics, unless the dealership has manual models in stock.