I built an MPCNC with the SKR3 board with the TMC2209 drivers and not the EZ insertable ones. My understanding is that this is purely a different socket plug and play approch for the drivers and this doesnt change the approach in the software.
I downloaded the platformio plugin within VS code to make the updates. The key issue is to make sure you have the correct chip set as they have changed this in time.
I uploaded the firmware and files to this post Configuring Marlin for SKR 3 EZ - #11 by andyc which you may find useful
this thread may also be helpful Configuring Marlin for SKR 3 EZ