[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/modules/contact-creation-manager/services/create-company-and-contact.service.ts

@@ -61,9 +61,6 @@ export class CreateCompanyAndContactService {
       await this.twentyORMGlobalManager.getRepositoryForWorkspace(
         workspaceId,
         WorkspaceMemberWorkspaceEntity,
-        {
-          shouldBypassPermissionChecks: true,
-        },
       );
 
     const workspaceMembers = await workspaceMemberRepository.find();