Yes, what you have given as your rule of thumb is quite clearly part of it, as well as the fact that with phrasal verbs used intransitively the problem never occurs - of course.
Yet, I wish we could come up with a little more. For example, I think that some of these particles are much more likely to be used as adverbs than as prepositions. Others work more often in the opposite way. "together", for example, is always adverbial, and thus separable: "put it together".
Possibly "apart" and "away" and "back" also have this property, but I have not done the research to find out. On the other hand, it seems to me that "into", "to", "from", "for", "with", and "without" do not normally occur preceded by an object pronoun: "to do without something", "*to do it without".
And then I suspect that cases of a phrasal verb followed by "with" (and there are many) are always inseparable ("to come up with an answer", "*to come it up with", "*to come up it with", but again, I have not done the research. Would you like to volunteer?