Originally Posted by
username
Doesn't OP's wife "already got her Taiwan Entry Permit from Taiwan"? They still would not let her fly to Taiwan? Lots of Mainland spouses, students and relatives fly to Taiwan directly from Mainland, even now.
No, to fly directly to Taiwan, China issues a permit called a 大通证, which needs to be endorsed to be valid. They currently don't endorse those permits for tourism (I presume that's the category that OP's wife has). What you mention about Chinese spouses, students, and relatives are on different visa types, which China will endorse.