I'm not surprised you are getting different answers to some of these, because this is just the sort of thing that tends to vary quite a bit by region. For instance, as someone raised in California, I say that I am "in line", meaning I am waiting in line. Others (I believe this is a northeastern thing, but I may be wrong) say "on line", which has always sounded very odd to me.
One of the reasons you get this kind of variation, I'm afraid, is precisely because there are no consistent rules. Or rather, I should say, that there are many cases where one or the other could be used depending on how you conceptualize the situation, and these are just conventional. For instance, in your bus example: on the one had you are definitely inside the bus, but on the other you have boarded and stepped onto (not on top of) the bus, so you can see how the latter may have come about.
For my dialect, it's: "good luck on" and "on the list".
Though I think both variants sound fine too.
In Ancient Greek, it is assumed that most, if not all, prepositions were once adverbs. That is why most prepositions can still be used as adverbs starting a sentence in Ancient Greek, as in "upon [that event], the King refused to...". If the same applies to the Germanic languages, it accounts for the existence of our ubiquitous phrasal and separable verbs, which still use "prepositions" in a non-prepositional way. The fact that new phrasal and separable verbs can still be created supports this hypothesis.
On a side note, the preverbial affix e- (the augment) for the past tenses in Ancient Greek probably came from an adverbial constituent **he* meaning something like "past" or "then". (There is evidence suggesting that this is cognate to the Proto-Germanic prefix that is used with past participles in German and Dutch, ge-, though others suggest instead that ge- is related to Latin con-, Greek sun-, "together". If the latter, I don't know whether **he-* would be related to con-/sun- as well. In any case, Old English used to have ge- as well, the vestiges of which can still be seen in many words, such as a-like (Dutch gelijk) and e-nough (Dutch "genoeg"). For more on the English prefix, see the question What we've gelost.)
It is my theory that most elements of syntax are relatively new (some post-Proto-Indo-European) and originate in separate words that melted with content-words and turned into affixes by clisis (enclisis, proclisis, etc). There is evidence that points to this for inflection: it is believed that, say, the dative ending -i was once a separate word, perhaps some postpositional adverb, which accompanied the direction of an action. Evidence for this might be the use of certain suffixes in Greek that are sometimes interchangeable with cases: -the(n) is mostly a (poetic) suffix of separation, which is normally expressed by the genitive; but it can often take on other functions of the genitive too, such as possession. And there are other suffixes that imitate partial cases: -de for direction (instead of accusative/dative/preposition), -(s)ô approximately for a forward position.
The birth of relative pronouns (classical hos) and demonstrative pronouns (classical houtos) in Ancient Greek is sometimes estimated to be not long before the time of Homer, because, in his epics, there is usually no difference in form between these pronouns and the article; it is often hard to decide on the interpretation of an instance of to (neuter article in classical Attic) or hos (masculine relative pronoun in Attic), when all three options seem possible for each (article, demonstrative, relative). This is evidence that syntax can also develop from differentiation between allophones/allomorphs, or out of nowhere.
Best Answer
You have understood one thing correctly: a preposition is combined with what follows it to form a prepositional phrase, and they form a single constituent in the sentence. Generally speaking, words in English govern (ie. control or specify) the words that come after them. In linguistics, we say that English is right-branching, meaning that new syntactic elements come after (to the right of, in writing) the elements that govern them.
Note that there are exceptions, such as adjectives, which precede the nouns that govern them. English is not exclusively right-branching, but it is predominantly right-branching.
But what does this have to do with prepositions? Well, just as a preposition governs the noun phrase that comes to its right, the preposition itself is governed by something to its left. And in many cases, that thing is a verb. English is full of idiomatic combinations of verb + preposition, where the verb requires a specific preposition to follow it, and anything else is an error. To take some obvious examples cribbed from other answers:
These combinations are highly idiomatic, meaning that the correct choice of preposition cannot be predicted simply by knowing the general meaning of the words involved. So the people who ask about what preposition follows a certain word are asking a reasonable and intelligent question. The choice of preposition very, very often depends on what came before it.