Hi @dirkt68 ,
The changes you are doing is correct.
To completely turn of the RAK4630, you have to remove both +3.3v and +Batt.
There is another option you can do which operate the nRF52840 in normal mode. I highly suggest you backtrack the discussion here - RAK4631 without baseboard
In normal mode, it will allow you to connect all supply in 3.3v voltage rail. No need to get bothered by the VBAT_NRF.
However, in your case, since you are developing custom PCB, it might be a good option too if you can switch from high-voltage mode to normal mode via jumpers/pad/resistor. Like on the design of RAK4630.
This resistor will allow you to switch from high voltage mode to normal mode depending on how and where the VBAT_NRF and VDD_NRF pins are connected. I think this is a more flexible approach and will be helpful on the proto stage of the design.