Well, yes and no (ain't that alys the way, tho). 'moku e kili' is a transitive verb and a direct object, 'lon ma Elopa' is a prepositional phrase, dba a verb. I'm not sure that should be enough to separate them, but it is in fact. tp just doesn't have a S=>NP transformation, so 'jan pi lon ma Elopa' comes about in a different way, probably by having prepositional phrases as modifiers directly and then deriving the sentential form from that.
'kama jo e mani li pona' is not grammatical for the same reason (well, a closely related one: 'e' can't occur in NPs any more than it can occur in modifiers). Word clumps (and they are basically not differentiated in tp) can occur in four places (leaving conditions out for the moment): before 'li', right after 'li', right after 'e', and right after a preposition. The significant thing here is that all these clumps are defined explicitly without either 'li' or 'e'.
Sorry, but relative clauses -- and we don't, alas, distinguish restrictive from non- -- all have to be done with two sentences. I do tend to put the restrictive clauses first and the non-srestrictive second but that is my habit (I think) and not any rule (it does make a certain sense, but I am sure the other does as well) "the person that took my bag is tall" jan li kam jo e poki mi. jan ni li suli. "A person, who is tall, took my bag" jan li kama jo e poki mi. jan ni li suli. (That example turned out to be just confusing. Sorry)