Ok here is how it works, depending on which mode the project is in:
read-only mode (means the project does not contain any custom Sk scripts or components - all Sk scripts are generated): The IDE does not launch by default, only when you hit the button. When you shut down UE4, the plugin remembers if the IDE was connected at the moment of shutdown (or crash). If so, it will launch the IDE next time you fire up UE4. If not, it will not launch the IDE.
editable mode (means the project contains custom Sk scripts or components): The IDE always launches by default to compile the scripts which is required before the compiled binaries can be loaded. However, it will launch either maximized or minimized, again dependent if the IDE was connected at the moment of most recent UE4 shutdown or crash. It also launches minimized if it was minimized at the moment it was closed. So if a team member prefers to work without the IDE, they would simply close it. It might still launch occasionally in minimized mode to compile the scripts though.
We’re still refining this workflow and are happy to listen to your input and suggestions!