Hi Stefan.
The remapping pins is not determined by the component.
You can tell if its a component issue, by creating a new project using BL0011 as a target, You don't need to own a BL0011 as you don't need to compile.
Add the component in question, then see if you can select different pins for the SPI.
If you can, then it's not a component issue, its either there should not be more than 1 pin selected or there is an issue with the fcdx file that will be stating what pins will be available.
For example with your target device the lines within 32F469Discovery.fcdx thai is dictating the pins you can use are:
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<spi remappable='3' name='SPI2' >
<clk af0='5' port0='3' pin0='3' />
<miso af0='5' port0='1' pin0='14' af1='5' port1='2' pin1='2' />
<mosi af0='5' port0='1' pin0='15' af1='5' port1='2' pin1='3' />
</spi>
<spi remappable='3' name='SPI6' >
<clk af0='5' port0='6' pin0='13' />
<miso af0='5' port0='6' pin0='12' />
<mosi af0='5' port0='6' pin0='14' />
</spi>
Note:
PortA = 0
PortB = 1
PortC = 2
PortD = 3
PortE = 4
etc.
I have selected SPI12 for the SD component.
Looking at <spi remappable='3' name='SPI2' >, I can see
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<clk af0='5' port0='3' pin0='3' />
Which is telling me only Port D3 is the only pin available when using discovery.
However with MOSI, within fcdx the code is
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<mosi af0='5' port0='1' pin0='15' af1='5' port1='2' pin1='3' />
Which means Port B15 & C3 is available.
You edit your own local 32F469Discovery.fcdx which is within
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%ProgramData%\MatrixTSL\FlowcodeV10\FCD\ARM\
I Don't know the reason for the restriction, it might be due to your hardware.
But at least now you have enough information to change the pin what is used at your risk, as changing the pin to one which is not within the datasheet will stop SPI from working.
My advice is check the datasheet first, and see what pins the SPI clock uses.