Multiplexing can have different meanings.
You are probably familiar with the concept of multiplexing several data streams over a single link, like what happens in TDMA, time-division multiplexing, where the overall data stream in split into timeslots, and each individual stream is mapped to one or more timeslots, like in G.703 (oh f*ck I’m old), SONET/SDH or GSM, for instance.
You have likewise CDMA (in wireless) or DWDM (on fibers) which are frequency-based, and many other similar schemes.
But on MCUs multiplexing has a completely different meaning. Yes, different signals can be routed though the same pin, but just not at the same time.
Depending on the chip, it may be very limited (pin X can use function A or B), or be a lot more flexible with a multiplexing matrix (you can assign functions A, B, C, etc. trough any of the pins X, Y, Z, etc.), and anything in between (matrix with restrictions on which combinations are possible or whatever).
In some cases you may be able to actually use both functions on the same pin (at different times), but that would require logic to make sure only the right peripheral is connected to that pin at the right time (so you need your own multiplexing on the outside of the chip). This is similar to the “chip select” used on some buses for instance.
What you do and how you do it may vary a lot based on the chip and your requirements. Maybe you can assign the two functions you need to two different pins (or sets of pins), which is the easiest. In some cases this just means switching from one bus/interface to another (e.g. you have multiple SPI or I2C interfaces, and you just switch to another one). In other cases you just have a conflict, and either you can resolve it through selection, or you just need to switch to a different chip.