Taiwan is a major US ally, so if this backdoor is real, then there will be trouble. It would be best for all parties involved for this to turn out to be a false alarm.
Taiwan is not a "major" US ally, rather the US is Taiwan's major ally. The US has several other regional countries it has a significantly greater alliances with, such as Japan, South Korea and Philippines. Though through an act of Congress, the US may (depending on the situation) have some obligations to aid Taiwan in its defense if attacked by mainland China.
As a random but relevant example, Foxconn is a Taiwanese company but much of its manufacturing capacity is on the Chinese mainland.
Taiwan is politically an ally of the US, but economically it is much more closely aligned with China.
"Renegade province" is the official stance, but you're right, it is much more complex. In practice Taiwan is autonomous, and the degree of interaction with the mainland is a big political issue -- there were no direct flights between Taiwan and the PRC until just a few years ago. And yet, as you say, Taiwan is economically interlocked with China.
It is interesting to see the discussion here and elsewhere focus on China as a bogeyman. I suppose the news fits into the narrative that has been constructed about Chinese espionage and such.
