Xoti's lantern and ghosts interaction
It doesn't make a gameplay difference whether a soul follows you or is put in the lantern.
Lorewise, if a soul follows you, it returns to the wheel after you visit an active Adra Pillar. If it's put into Xotis lantern it is released by whatever method you chose for xoti at the end of her companion quest.
The number of souls in her lantern are only relevant once, namely, you need to get enough souls in there to trigger the quest continuation (around 10). There are enough wayward souls on Port Maje alone to trigger this.