It's a deliberate policy that I do not provide any 'live flight tools' in UAV Toolbox. Whilst it would be possible to replicate the Yuneec Flight Mode app, I cannot test as thoroughly as Yuneec in all possible conditions and their tools are fine for the job of flight control. So UAV Toolbox is designed to get out of the way of Yuneec software at the critical time.
Now, if the SDK that Yuneec plan to release includes a tested flight stack that can be incorporated into third party apps, I'd be happy to use it - as I assume that they would cover any problems you might encounter during flight.
However, in general there's no reason why they should warranty against unreasonable modifications or poor maintenance of your equipment. If you fill the ST-16 full of Candy Crush Saga and Facebook Messenger, or paint your rotors with garage paint, they'd have every right to refuse to fix the problems that would ensue. If you install a third party app, you should take a moment to consider what it might do that would cause problems, and what the developer has done to test the app.