They are qualified but the reality is that they just can't do it, and Lexus won't accept them as doing it even if they do.
So, essentially, if you go for the Toyota Service, you would need the hybrid health-check for that extra 1 years warranty on the hybrid system so cost won't be that different.
Additionally, I'd be very very wary of warranty direct - there's a lot of things that they don't cover and I bet they won't cover a hybrid failure. Additionally, I don't think they're much cheaper than Lexus warranty which comes with roadside assistance included
The Lexus warranty is actually very good - probably one of the better warranties out there.