[Clark]

Spacious prepositions are really a hard nut to crack. Sometimes one and the same picture can be described by using different prepositions. The thing is that language does not reflect reality as it is, it reflects our vision of reality. When one hears 'There is a bird in the tree', they imagine the bird inside the crown of the tree. When one hears '... a bird on the tree', they imagine it on the surface of a tree branch. A spacious preposition serves as a special cognitive instrument by means of which we conceptualize what we see.
A language may determine the way we look at the outside world. Sometimes even within one language, perception concepts may vary from one group to another depending upon the climate, relief, traditions, history and other factors. For example, the British traditionally say 'in the street', whereas the Americans say 'on the street'. 'A street' for a Briton is a road with the facades of the houses on both sides. That's why 'in' is used - 'within an enclosed space'. For an American 'a street' is just the flat surface of a road only, and that accounts for 'on'. There could be historical and architectural reasons for that.
I can't say for sure, but it might be a similar thing with ' fruit/monkey on vs. in the tree'.
If you are writing a thesis on 'in/on + vehicle', it may be useful to look into the history of the English language. Which preposition was used when the first buses appeared? What did buses look like in those days? Did they look like a platform? How was the preposition usage changing as time went by? etc. In carrying out semantic research it is always good to combine the synchronic and the diachronic aspect.