Both the PHandle and Pin control mechanisms for configuring GPIO pins have standard configuration flags. This was different with the (now deprecated) -pin pin assignments, which had an ad-hoc scheme for configuring mechanisms like pull-up resistors. To support users still working with the nRF Connect SDK v1.x, this legacy representation will now work properly in the pin configuration interface.
If a node has at least one such legacy -pin configured, this format is used for the node and the pinctrl format is filtered out. If pinctrl is available and there are no legacy -pin pins, the legacy pin definitions are filtered out.
The output and drive buttons are disabled for legacy pins, as they did not have a mechanism for this in Devicetree.