Sara
This is my representation of the GPIO and PORT interaction:

The interesting part is that if the GPIO function is not selected (eg. the UART is connected to the pin in the PCR MUX setting) the PDIR register still reflects the pin's state, which suggests that the PDIR is always connected to the pin, so reading the state is always possible.
When the PORT doesn't select GPIO mode it is not possible to control the pins state as an output (this is obvious).
The PORT module controls also pin interrupts and DMA (not your KL03 but most other devices), which can operate irrespective of the pin's multiplex function.
Always read the GPIO instantiation description for deviations and reset defaults:

In case of doubt is is best to experiment. I do this with a built in memory debugger but you can do it with SWD debugger if you don't have such capabilities build into your project. Eg.
md 40049000 l 32
Memory Display
0x40049000 00000706 00000203 00000203 00000703 ................
0x40049010 00000707 00000202 00000000 00000000 ................
0x40049020 00000000 00000000 00000000 00000000 ................
0x40049030 00000103 00000005 00000001 00000001 ................
0x40049040 00000004 00000001 00000005 00000005 ................
0x40049050 00000005 00000000 00000000 00000000 ................
0x40049060 00000000 00000000 00000000 00000000 ................
0x40049070 00000000 00000000 00000000 00000000 ................
This display the PORTA register settings, where PTA5 is set as an input peripheral function with pull-down enabled.
md 400ff000 l 7
Memory Display
0x400ff000 00000000 00000000 00000000 00000000 ................
0x400ff010 0010101a 00000000 00000000 ............
This is the GPIOA register set, where the PDIR is showing that a '0' is read at PTA5
mm 40049014 l 203
Write - OK
Here PORTA_PCR5 modified to have a pull-up resistor active.
md 400ff000 l 7
Memory Display
0x400ff000 00000000 00000000 00000000 00000000 ................
0x400ff010 0010103a 00000000 00000000 ...:........
It is seen that the PDIR sees that the input is not at '1'.
Regards
Mark
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