As of v1.0.0, the "Compile with PL/Scope" action changes the plscope_settings parameter in the session, then recompiles objects in the schema (unless the user has opted out of that), enforcing whatever PL/SQL compilation parameters are effective in the session when doing so.
The expectation is that it would preserve prior PL/SQL compilation settings for all affected objects, with the single exception of updating the plscope_settings parameter.
This is important because some modules could have specific requirements as regards compilation settings (especially, but not limited to, the value of the plsql_ccflags parameter), and these settings should not be lost when running the action.