It was because of Merlin.
Everyone in the exploration team was aware that the one who contributed the most wasn't the Archmage, Suyass, and neither was it the leader, Lys. The one who contributed the most was the young Great Mage who joined the team with his two subordinates and had the loot priority on all magic materials.
Fran hadn't been the only one to complain. At first, a few of the leaders of Thousand Sails City's forces also disapproved. However, they hadn't insisted on it because the Gilded Rose was formidable and no one dared to offend that young Great Mage. Even if they didn't agree, they consoled themselves, thinking that at least they would get to improve their relationships with the Gilded Rose.
But as the expedition got further and further, everyone could see that letting the young Great Mage have loot priority wasn't unfair.