Let's break the sentence
If the Chinese were doing anything except what they're doing
into two parts.
The latter part, "what they're doing" refers to their convoluted and counterproductive approach at building a commercial plane.
"If the Chinese were doing anything except" means that were they building a plane with a different (uncomplicated and productive) approach, it would give the western manufacturers -- Boeing and Airbus, as mentioned in the actual article -- reason to be terrified for the loss of sales.
The reason that the writer thinks that their approach is convoluted and at times unproductive is listed here -
First, he believes the heavy hand of a state-owned enterprise is the wrong approach to cracking into the global commercial aircraft business. Second, he maintains that partnering with Western equipment manufacturers under preconditions such as a requirement of Chinese manufacturing will add risk and ultimately not bring the most current technology, due to intellectual property concerns.