Problem with using civilian airline on a regular route is that it is legal. The only "illegal" one is the passenger onboard the aircraft. And that is only illegal according to China's law in Chinese airspace including Taiwan. It would be controversial if PLA intercepts it or block it in international airspace (not counting Taiwan airspace). Theoretically, without going into war with US, PLA can only intercept it after it has entered Taiwan airspace and force it to turn away.
You forget there is no such thing as Taiwanese airspace, only Chinese airspace, over the island of Taiwan.
If Pelosi goes on a civilian airliner and said airliner gets instructions from military fighters, no sane or responsible airliner pilot would disobey. Their first and primary responsibility is their duty of care for the safety and wellbeing of their passengers, and they are not going to risk a shootdown just to prove some geopolitical point.
If Pelosi tries to go to Taiwan secretly on a civilian airliner, I think the PLAAF will escort it until it crosses the 12nm territorial airspace limit and then order the pilot to divert to a mainland Chinese airport, where police will be waiting to arrest Pelosi for illegally entering China.
TLDR, trying to sneak into Taiwan secretly on a civilian airliner is going to be a spectacularly bad idea for Pelosi.