I would think the reason they did not use the small compartment in the movie was that it would be virtually impossible to shoot the scene in that crammed space.
About space above the shelf, that's a good question.
Here's a picture from a different type of coach, with a different interior but based on the same basic structure.
As is obvious, the space above the racks is quite high towards the middle of the coach. It should be sufficient for the trunk to open.
I subscribe to the idea that Oskar got help from a co-passenger to get the trunk onto the train and up on the luggage rack. However, part of some of the platforms at Stockholm Central Station are indeed under a building, and thus shielded from direct sunlight. I have toyed with the idea that Eli helped Oskar with the trunk, and climbed into it only after it had been placed on the luggage rack.
About Oskar being in risk of recognition, I think this might not be so. Stefan Larsson, for one, did not recognise Oskar at the train. I would think this is quite plausible, on the grounds that the identity of Oskar might not have been revealed to the news media already in the morning of the 13th. The police would plausibly have preferred to keep such information to themselves, since the investigation had just started.
There is also a slight possibility that the police didn't understand that Oskar had disappeared until sometime during the 13th. It very much depends on what Oskar's mother did when he didn't return back home. Earlier that night she had learnt that Oskar had ran from his father a few days earlier, and then spent the night at an undisclosed place. What would she think now? That he had ran off to that place again? Where, then, would Oskar be? At a schoolmates home, perhaps? She would likely have a list of all of Oskar's classmates, and maybe she would eventually start calling them. Or maybe not, if she waited too long. She would not want to wake up strangers to ask for her son. But she might not want to call the police either. What would they be able to do, if Oskar was at the home of some classmate? So maybe she just sat alone through the night in anguish, unable to act.
The boys at the pool would have wanted to get home ASAP, and on their way they would have found Mr Ávila in the dressing room. If he was still unconscious they would likely have though that he was dead, and left him there. If he instead was awakening, some boys might have stayed behind to help him. Those boys might have called for help from Mr Ávila's office. Otherwise, the police would have eventually been called by the boys' parents.
Upon arriving, the police would have found either Mr Ávila alone, or with some of the boys. They would also have found the shredded corpses of Jimmy and Jonny. I think it would be quite likely that the fact that Oskar had disappeared might go unnoticed by the police quite long, since if not all, at least several of the boys would already have have left for home when the police arrived.
Thus, if Oskar's mother didn't call about Oskar, the police might not have learnt about his disappearance until the 13th, when they had interviewed some of the boys. However, if they knew about it, they still might not have wanted to disclose it to the media before interviewing the witnesses, i.e. the boys.
All in all, I think it's rather likely that Oskar didn't appear in the news until the 14th.
