Speaking as someone who is familiar with some parts of the Firefox architecture or concepts thereof, but not the source code itself: If you were to implement per-container pref overrides, theoretically yes. AFAIK, prefs are global right now. I don't know if it's feasible to implement this in Fx or if that will leak through to the chrome (process).

But it's an interesting idea! Would you mind filing a bug at bugzilla.mozilla.org?