I have checked this using the last version of CubeMx (4.13.1), and I do not see the issue that you have mentionned; every thing goes well and PA9 is well selected by default as USART_Tx.
So Maybe you have used an old version of CubeMx ?
Try with this last version of STM32CubeMx (4.13.1) and hopefully your issue will disappear.
I have attached the .ioc of th test project That I have used.
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