You're right about Napoli's size putting pressure on managers. Its a big decision, especially given Gasperini's current situation. Napoli has superior resources and players over Atalanta. But Gasperini's constructed something exceptional at Atalanta. Teamwork and coherence are hard to reproduce. With Napoli in such trouble, is it time to abandon ship? Managers will feel pressure to turn things around quickly, which is difficult. It depends on what Gasperini loves most: the chance to challenge himself or his stability and success. A true brain-scratcher.
Napoli can provide better chance for Gasperini if he wants to aim at a higher level for his coach career as he is no longer young and his coach career will not last for too many more years. Napoli and Atalanta can be considered the same that no guarantee that they can consistently join Champions League. Each season, they have to compete with many other clubs that have nearly similar quality, to be qualified for Champions League.
It's not clear that either Napoli or Atalanta can be strong enough to be sure that they will appear in top four or top five of Serie A season by season. Gasperini will have bigger budget for player transfer in Napoli but challenge will be nearly as same as in Atalanta because of two clubs' quality is nearly the same.