By using the phase jitter between the DFLL48M clock and the FDPLL96M clock.
Even if both use the same reference source, they have a different jitter.
SysTick is driven by FDPLL96M, the us counter by DFLL48M. As a random
source, the us counter is read out on every SysTick and the value is used
to accumulate a simple multiply, add and xor register. According to tests
it creates about 30 bit random bit-flips per second. That mechanism will
pass quite a few RNG tests, has a suitable frequency distribution and
serves better than just the time after boot to seed the PRNG.