flying out from a different city

Actually, you are allowed to depart from a different city, but Wenzhou airport, although within eligible Zhejiang province is not an eligible port of entry/exit to/from Shanghai transit area. In other words, you are perfectly allowed to explore the entire City of Shanghai and entire provinces of Zhejiang and Jiangsu, Wenzhou included, but the airports that can be used at the time being are: Shanghai Pudong, Shanghai Hongqiao, Nanjing and Hangzhou. Starting from December 1 also Ningbo airport will become eligible entry/exit port, but Wenzhou not.

To conclude, you cannot use Wenzhou for your onward flight to Taiwan, but you can use Hangzhou if you prefer not to return back to Shanghai. Anyway, to be allowed to use any of the airports, you have to decide for a particular airport and have a ticket out of it, even before your arrival in Shanghai transit area.