arm: dts: imx8mp-beacon-kit: Resync DTS with Linux 6.8

The device tree has evolved over time, so re-sync.  This also
partial reverts one change on the PCIe, because U-Boot doesn't
have a proper driver.  However, since the clock is configured
to generate a 100MHz reference clock by default, a proper driver
isn't really necessary.

Signed-off-by: Adam Ford <aford173@gmail.com>
Acked-by: Peng Fan <peng.fan@nxp.com>