I'm really speaking for the entire downtown section, Exhibition to East Harbor. Soil settlement isn't really a big issue there, yes, but clearances still exist. We are tunneling under/between 2 active subway lines, PATH, and a network of sewers, watermains, gas lines, and oil lines we haven't fully mapped. Vibration concerns/dynamic loading on these existing structures is a huge cause for concern, so in this case, you're probably right that it won't be worth it building the subway at a higher elevation without utilizing cut & cover. That being said, there is still the possibility that it might be cheaper to tunnel a few meters higher using a narrower tunnel while incurring the risks of damage to existing infrastructure, so it can't be ruled out altogether (during initial design phases).
Regardless, if the IBC of the Relief line stated that it was best to deep bore this thing, the OL will have to be deep bored as well, especially if the tunnels are wider.