The comma is a choice of style. Some style books say it depends on context, others recommend one option or the other.
Those prepositions are simply prepositions. They aren't conjunctions in any way. Whether or not you can move a phrase is not directly related to whether it is a clause or not. I have to admit I don't understand your explanation of why you think they should be conjunctions. Many kinds of phrases are separated from the rest of the sentence by one or two commas without being clauses.
A clause is a finite verb and all its arguments, i.e. a main verb and everything that depends on it. If you have a sentence with a single main verb, the entire sentence is one clause. Conjunctions and relative pronouns typically introduce new clauses.
In the Odyssey, Odysseus poked out the eye of the Cyclops.
The sentence above has a single clause.
The Cyclops whose eye he poked out was named Polyphemus.
Here are two clauses: the entire sentence is the main clause; part of the main clause is the subordinate whose... clause. Each clause has its own finite verb: poked and was. Here whose is a relative pronoun, which always introduces a subordinate clause. This relative clause is defining/restrictive, in which case it is not marked off by commas.
Subordinate clauses are technically part of a main clause, but, in practice, when one says "the main clause", one often means "the main clause excluding its subordinate clauses". Note that some linguists consider any verb to be the core of a clause, not just finite verbs; but I will not do so here.
He maimed the Cyclops but didn't kill him.
Here you have two main clauses. Notice that they can't be moved around, which is usually the case with two coördinated clauses. But is a coördinating conjunction, which means it introduces a clause at the same level, in this case a second main clause.
Troy he no longer thought of.
He no longer thought of Troy.
The object Troy can be moved around. The result is a change of focus. It is obviously not a clause.
Solemnly Eurycleia washed Odysseus's feet.
Eurycleia washed Odysseus's feet solemnly.
The adverb, which isn't a clause, can be moved around.