A skull cradled in a saint's hands can look, to a modern eye, like a morbid flourish added for atmosphere. Within the monastic culture Zurbaran was painting for, it was closer to an instrument, a physical prop used in a specific, deliberate spiritual exercise called memento mori, remembering that one will die. Monks and nuns in several Christian orders kept skulls in their cells for exactly this purpose, objects to be looked at and held during prayer so that the certainty of death stayed present rather than comfortably abstract.
The logic behind the practice connects directly to the vow of celibacy and world renunciation this article's companion piece is filed under. If a monastic life is built on giving up marriage, family and possessions in favor of total devotion, then constantly remembering that every earthly attachment ends in death was understood as reinforcement for that choice, a daily reminder of exactly what was and was not worth holding onto. Francis is not shown recoiling from the skull or displaying it outward for a viewer's benefit. He holds it close, against his own chest, in a private act of contemplation that has nothing to do with anyone watching.
Zurbaran painted this kind of composition, a single robed figure, a skull, an empty background, for monastic patrons repeatedly across his career, refining it into something close to a formula. That repetition was not a failure of imagination. It reflects how central the memento mori exercise actually was to the devotional life these paintings were made to support, a practice worth returning to again and again rather than illustrating just once.