It sounds like you are alluding to some warranty issues due to the aftermarket controller. Would you care to share your thoughts?
You've just given the manufacturer a loophole not to have to deal with you. However, what's odd is that for whatever reason this t-stat seemed to solve your legitimate complaint. If I would have gotten involved in this issue, I would want to know how and why this controller fixed your issue. That said, it sounds like Lennox didn't want to have anything to do with this issue, or at least give you a direct answer.
If something is wrong with the equipment and it's a legitmate issue which no one can explain, it would drive me bat crap crazy.
Thing is, sometimes it's impossible to tell without a jobsite inspection. BUT... that's what facetime is great for, service calls direct with the manufacturer or their technical reps.
That said, some mini split manufacturers do have the option of wiring in any 24V conventional t-stats to them.
Again, tell your installing contractor to deal with either Daikin, Fujitsu or Mitsubishi down the road. Much better contractor support IMO across the nation. All 3 have been in the game in the US very long, and they all do hands on factory training for the contractors, and all came from Japan. Ironcially enough, Daikin sooner or later will probably be the first to be able to claim "made in the US" with thier residential single phase mini splits.