From just seeing the will, and having a possibly misguided interpretation on medieval hereditary primogeniture, it looks like we could assume that William simply valued the Duchy of Normandy higher than the Kingdom of England. But perhaps there is more to it than that?
There are a few layers to this answer.
The most obvious - but not necessarily the most important - is that William and his eldest son Robert did not get along. In fact, Robert had led a rebellion against William and it was only through the intercession of Matilda of Flanders (William's wife and Robert's mother) that they ended their feud. Robert was seen by most, including his father, as weak-willed and lazy; someone who could be easily controlled by those around him.
But more importantly, Normandy had a particularly interesting variation of primogeniture. It was tradition among the dukes of Normandy that the eldest son inherited the family lands, and that the second son inherited anything gained through conquest or marriage. Any other sons would be given small parcels of land, money, or be committed to the church. ^1
So it's logical, though very unusual, that Robert - the eldest son - would inherit the "lesser" title of Duke of Normandy, as it was the family holding. William's second son, Richard, had died around 1075, leaving William Rufus as the logical inheritor of England, which had been gained through conquest.
Even with this tradition though, William wanted to disinherit Robert. He was only convinced on his deathbed to abide by the tradition and allow Normandy to go to Robert. It's possible that William was convinced of this by supporters who knew that they would be able to control Robert should he inherit.
So, it's a combination of legal precedent, animosity, and back-room dealing that let to the eldest son inheriting the Duchy of Normandy, and the next son the Kingdom of England.
^^1 HANLEY, CATHERINE. "CRISIS IN ENGLAND." In Matilda: Empress, Queen, Warrior, 35-51. NEW HAVEN; LONDON: Yale University Press, 2019.
Normandy was a vassal territory to France that William had fought to keep and essentially held with more autonomy than he was meant to have afterward.
His first son Robert had a few good points, but he consistently fell back on his bad points. He had demanded Normandy of William while William still lived and was declined, and he also felt slighted by his father in general. He also noted, rightly, that his father favored his brothers more. He rebelled against his father and with help of Matilda, William's wife and Robert's mother, they eventually reconciled. Their relationship grew worse again when she died, and he was tempted to give Robert no inheritence but was counseled to grant Robert at least one of the major holdings. So William gave Robert Normandy, he gave his favorite and [to his mind] more reliable son William the Kingdom of England, and for lack of other major territory gave his youngest son Henry money. He might have preferred to give Henry Normandy, or even give William both territories but it would have certainly caused a familial war which nearly happened anyway when Robert tried to make a pass at the English crown.