[permissions] fix workflows + remove shouldBypassPermissionChecks for system objects (#12559)

In this PR 

1. fix workflow step creation by adding forgotten
`shouldBypassPermissionChecks` in WorkflowVersionStepWorkspaceService
2. clarify the rule for twentyORMGlobalManager: do not add unnecessary
`shouldBypassPermissionChecks` for system objects (there are no
object-records permission checks on system objects, they are dealt with
at resolver level)

packages/twenty-server/src/engine/core-modules/auth/strategies/jwt.auth.strategy.ts

@@ -76,9 +76,6 @@ export class JwtAuthStrategy extends PassportStrategy(Strategy, 'jwt') {
       await this.twentyORMGlobalManager.getRepositoryForWorkspace<ApiKeyWorkspaceEntity>(
         workspace.id,
         'apiKey',
-        {
-          shouldBypassPermissionChecks: true,
-        },
       );
 
     apiKey = await apiKeyRepository.findOne({