I have not seen the TV show, so I have no idea if there is a 'specific bathroom' in this forest or not. And it doesn't really matter.
Native speakers say the bathroom when it is reasonable to suppose that a bathroom exists in a given building, including a house. By extension, a native speaker could say the bathroom to refer to 'any bathroom that Naruto went to' because that is the bathroom that he went to.
Choji could have said a bathroom but it would not have been idiomatic.
While we are on this subject, you should also be aware that go to the bathroom has two meanings in English. One is the literal meaning: travel to the bathroom. The other meaning is figurative, and it means to urinate and/or defecate. For example, in this passage, go to the bathroom has the figurative usage:
It's disgusting to even contemplate what might happen if an astronaut in space tried to use and flush a regular toilet. So how do astronauts go to the bathroom in space?
Notice that the title of the article itself, How does going to the bathroom in space work? uses the figurative meaning. So does the YouTube video entitled The Nylon Swish - How do you go to the bathroom in that?!
As for a ceiling, yes we might expect the ceiling if talking about a ceiling that the listener can identify, but a ceiling is also possible. It depends on the speaker. It's important to note that both the definite article and the indefinite article can refer to specific referents. When refering to a specific referent, the difference between the two articles is whether a definite reference or indefinite reference is made.
For another example of this, consider the following two sentences:
Watch out! A train is coming!
Watch out! The train is coming!
Both sentences refer to a specific train that the listener can identify (namely, the one coming down the track that the speaker is warning the listener about). But it's up to the speaker whether he wants to use the indefinite article or the definite article.