It's interesting how Cool-sensei handles this. He is usually not very subtle, but Elma's situation has actually been treated really well.
My assumption is of course, as many said, that Elma has feelings for Tooru. There have been quite a few hints across the manga already, but especially in the last volume it has been really heavily implied.
That is also why Elma apologized imo. She understands that Tooru loves Kobayashi and she assumes Kobayashi also loves Tooru. So her allowing Elma and Tooru to travel around on their own far away from Kobayashi would require a lot of trust (because she believes Tooru would never betray her). But Elma knows that one day Kobayashi will be gone and if she sticks with Tooru she may one day not be able to contain those feelings anymore. She has all the time in the world after all.
PS: Tooru is an amazing chef now, so Elma's "preference" actually really works with her lol
PPS: Although not handled as well, I do like the implication that Kobayashi is looking at Elma and other girls more "like a man". It's not great phrasing, but I think Cool-sensei wants to imply that Kobayashi is developing a romantic/sexual interest in them, ever so slowly.
