STM32F4 USART Receiver Pin Configuring
Well, I'd say the basic structure picture tells you why this might work:



There is no block which would allow the selection of the digital input only going to the input data register or the alternate function input. So a pin configured as digital input will also send the data to the connected alternate functions.

The only option there is to have the schmitt trigger on or off, but that turns off the whole digital and alternate input then.

I'd still use the alternate function setting, because that is the intended way to use it and as long as no official source tells us otherwise I'd stick to what the manufacturer says (well except it doesn't work and you work out a workaround).