You don’t need to add pinmux setting dts to kernel dts. But you can check/compare/add the gpio dtsi to your kernel dtb. That would make sure gpio setting is by default output high or output low, or as input.
Are we talking about a custom board here or devkit?
Also, since jp5 is just developer preview, how about you firstly test these on jp4.x first? This could prevent unnecessary bug.