I've tried to go through the initialization code using DotPeek and think I see an issue there (if I interpret the flow correctly).

In an InitalizationModule for Commerce, a new folder of type SalesCampaignfolder is being created under the RootPage: 

private static void RegisterContentRoots(InitializationEngine context)
    {
      ContentRootService instance = context.Locate.Advanced.GetInstance<ContentRootService>();
      IEnumerable<IContent> items = context.Locate.ContentLoader().GetItems(instance.List(), new LoaderOptions());
      Guid sysCampaignRootGuid = new Guid("48E4889F-926B-478C-9EAE-25AE12C4AEE2");
      Func<IContent, bool> predicate = (Func<IContent, bool>) (x => x.ContentGuid == sysCampaignRootGuid && x.Name.Equals("SysCampaignRoot"));
      if (items.Any<IContent>(predicate))
        return;
      instance.Register<SalesCampaignFolder>("SysCampaignRoot", sysCampaignRootGuid, (ContentReference) ContentReference.RootPage);
    }

In the Register function Save is being called if the content is not already existing:

public override void Register<T>(
      string rootName,
      Guid contentRootId,
      ContentReference parentRoot)
    {
      Validator.ThrowIfNullOrEmpty(nameof (rootName), rootName);
      ContentReference contentLink = this._contentRootRepository.Load(rootName);
      if (ContentReference.IsNullOrEmpty(contentLink))
      {
        T content;
        if (!this._contentRepository.TryGet<T>(contentRootId, out content))
        {
          content = this._contentRepository.GetDefault<T>(ContentReference.IsNullOrEmpty(parentRoot) ? (ContentReference) ContentReference.RootPage : parentRoot);
          content.ContentGuid = contentRootId;
          content.Name = rootName;
          this._contentRepository.Save((IContent) content, SaveAction.Publish | SaveAction.SkipValidation, AccessLevel.NoAccess);
        }
        this._contentRootRepository.Save(rootName, content.ContentLink.ToReferenceWithoutVersion());
      }
      else
      {
        T content;
        if (!this._contentRepository.TryGet<T>(contentLink, out content) || !(content.ContentGuid == contentRootId))
          throw new NotSupportedException(string.Format("There is already a root registered for name '{0}' with id '{1}'", (object) rootName, (object) contentLink));
      }
    }

I assume that the call to Save that's being called in this case is the one that sends "SaveAction.Publish | SaveAction.SkipValidation" (the exception message also points in this direction).

public override ContentReference Save(IContent content, SaveAction action, AccessLevel access)
    {
      if (content == null)
        throw new ArgumentNullException(nameof (content), "Parameter is empty");
      if (content.IsReadOnly())
        throw new EPiServerException("You cannot save a content that is read-only. Call CreateWritableClone() on content and pass the cloned instance instead.");
      action.ThrowIfInvalid(nameof (action));
      StatusTransition transition = this._statusTransitionEvaluator.Evaluate(content, action);
      DefaultContentRepository.CheckStatusTransition(transition, content, action, nameof (action));
      action = DefaultContentRepository.StandardizeSaveAction(action, transition);
      if (access == AccessLevel.Undefined)
        access = this._requiredAccessResolver.GetRequiredAccessLevel(content, transition);
      if (transition.IsNewContent())
      {
        this.ValidateContentTypeAvailability(content, content.ParentLink);
        this.InitializeSortIndex(content as PageData);
      }
      content.ContentLink = this._versionResolver.Resolve(content, action);
      SaveContentEventArgs saveEventArgs = this._contentEventsHandler.CreateSaveEventArgs(content, action, access, transition);
      bool isNew = content.IsNew();
  ... Code removed due to readability
    }

Then I'm a bit confused to why the the exception that's being thrown comes from the function called "ValidateContentTypeAvailability"? I would assume that the flag SaveAction.SkipValidation would skip this validation step?

Maybe this should be registered as a support ticket to Optimizely?

/Martin

OK, an update about this issue. I found this forum post which mentions a similar problem: https://world.optimizely.com/forum/developer-forum/Commerce/Thread-Container/2021/11/episerver-commerce-upgrade-to-version---12-17-2---error---commercereportingfolder-is-not-allowed-to-be-created-under-parent-of-content-type-sysroot/. 

When looking for an appropriate place to add that specific code I found code where we explicitly set that one of our own page types are an (only?) allowed content type under the SysRoot-page. I guess this caused this error to occur to begin with. 

Good investigation!

One possible explanation is that in your local machine, the EPiServer.Commerce.Initialization.InitializationModule was executed before your module, while it was excuted after your module on test. If two initialization modules are not depend on each other, their order of execution is undetermined. Of course, just a guess.

Regarding your (2) point - it seems arguable that SkipValidation should skip all validations, or certain validations. I can raise the question to Cms team who wrote the current code. 

Thanks for bringing that question forward to the CMS-team Quan! I actually also started a support case (with id 1173786) when I didn't get any response in this question here on the forum if you want to connect the issues with each other. 

I know it's off topic from this initial question here but I mention it also in the support case that now when I've managed to get past this issue I stumble upon the issue mentioned here: https://world.optimizely.com/forum/developer-forum/Commerce/Thread-Container/2018/7/getting-error-when-loading-commerce-catalog/. I get this message when trying to load the Commerce Catalog:

I've tried adding my account to the Administrators-group and run the migrations but still no success, do you have any suggestions about how to fix this issue? 

The feedback is