Hi,
Thanks for letting us know. Yes, the after-initialization commands are indeed executed after ALL of the commands from the debug method.
As a better workaround, you can define a variable like “com.yourname.init_mcu” in your custom device definition and then add $$com.yourname.init_mcu$$ to the startup commands in the EDP. Then you won’t have to hardcode the device-specific commands in the EDP file.
We currently don’t have any plans for changing the current behavior as it looks like a fairly rare scenario and the workaround is also very simple, however if you believe it’s a big annoyance (or anyone else encounters a similar issue), please let us know so that we could reconsider this.