I’ve just run into this same issue. If I do a package of a MyProjectGame target on a clean checkout with nocompileeditor then the plugins are missing. If I build the MyProjectEditor target then do a package with nocompileeditor it works.
I think what is happening is that BuildCookRun needs to run the MyProjectEditor target as part of the UnrealEditor-Cmd calls to cook - so the plugin error occurs when the game-specific dynamic libraries (including plugins) that are built by the MyProjectEditor target are not present during the UnrealEditor-Cmd. That build step is what is suppressed by nocompileeditor
Is -nocompileeditor` incompatible with a clean BuildCookRun command on a project with plugins?
The answer is yes, it is incompatible. BuildCookRun needs to call UnrealEditor-Cmd to cook which uses project-specific dynamic libraries that are only built by the editor target (YourProjectEditor). These dynamic libraries are not built by the other targets (YourProjectClient, YourProject, YourProjectServer). Those other targets use static libraries / monolithic builds, which is what is created and linked during the actual game build step (different from the editor build step).