Ok here is an update. I wanted to build a poky image for beagleplay and have the uart5 working. I did get the image build and booted using the (default) arm-poky-eabi. The serial console was up, but not networking. The uart5 was occupied by the mikrobus.
I removed the uart5 from the mikrobus node in the dts, and configured it similiar to uart0. When booting from the SD, the new dtb was not picked up for some reason!, the one on the eMMC was loaded. So I had to add a /extlinux/extlinux.conf on my SD boot partition and also place the new dtb there.
LABEL beagleplay-SD
kernel /Image
fdt /k3-am625-beagleplay.dtb
APPEND root=/dev/mmcblk1p2 rootwait rw rootfstype=ext4 console=tty1 console=ttyS2,115200n8
Now this extlinux.conf is correctly loaded during boot. The uart5 gets linked to ttyS0 and works. The eth0 now also works as a bonus! And, I can boot from the SD card without pressing the USR button.