Count Adhemar is right. It is definately not RAI, but it works RAW. Here is why.
we have what probe says (if wound is delt in the assault phase, get pain token). We have what the siphon says (if you deal a wound, get a pain token) In 5th ed when the book was made, these two rules were independent and would have no problem working the way they were intended (you kill a model in shooting, pain token. You kill a model in assault, pain token)
The problem is with the rule change, we have this conflict. Why it works is simple:
Is overwatch in the assault phase? Yes
Do you overwatch with the Siphon? Yes
Did you do a wound with the Siphon? if yes, pain token is created
Was that wound in the assault phase? Yes... so pain token created
I know it sounds janky, but in reality its not that big of a deal. And like eohall pointed out, is it that hard to imagine fluff wise the Chronos killing two people with his flamer, then quickly running up and stabing it to steal its last essense???