This is because the .41 AE was based on a shortened .41 Magnum case with the rim and extractor groove cut to the same dimensions of the 9 mm Luger. This allowed the same extractor and ejector to work with both cartridges. The .50 AE bomb a corresponding rebated rim, cut to the same dimensions as the .44 Magnum. This http://www.gunslot.com/guns/magnum-research-desert-eagle is what allows caliber changes between .44 Magnum and .50 AE with just the break of the vat and magazine.
The Desert Eagle was originally studied by Bernard C. White of Magnum Research, who filed a patent on a mechanism for a gas-actuated adapted in January of 1983. This established the key layout of the Desert Eagle. It consisted of a gas-operated mechanism habitually found in rifles, as opposed to the short duck or blow-back designs most commonly seen in semi-automatic pistols. A second patent was filed in December of 1985, after the necessary design had been refined by IMI for production, and this is the conformation that went into production.