In answer to the question in $SUBJECT:

the "whole" pinmux configuration, yes.  But
Quite a lot of it can also be derived from
driver configuration.  (Which is board-coupled.)

So (a partly made up example) if a given SPI
bus is configured, with two chipselect lines
active ... that rules out PINMUX configs here
the MOSI/MISO/SCK lines for that SPI bus are
not muxed out, or where those chipselects are
unavailable.  (Unless the chipselects are done
using GPIOs, which is a driver/device config...

the board-specific code in the second-stage
(post-RBL) boot loader sets up PINMUX,
 as I recall, but Linux could do that based on
the devices configured (as sketched above), or
even just sanity check what it's given by that
second stage loader.

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