This can be considered a bug. However what is the right way to do it is up to discussion. I'll file a bug so we can discuss and will get back to you.

In the meantime, you can resolve that issue by creating a new editor descriptor for it.

Let's do it as following steps:

Create editor descriptor class

[EditorDescriptorRegistration(TargetType = typeof(ContentReference), UIHint = "TopLevelProductVariation")]
public class TopLevelProductVariationReferenceEditorDescriptor : ContentReferenceEditorDescriptor<CatalogContentBase>
{
    public TopLevelProductVariationReferenceEditorDescriptor()
    {
        ClientEditingClass = "your-dojo-client-resources-folder/widget/TopLevelCatalogContentSelector";
    }

    public override string RepositoryKey
    {
        get { return CatalogRepositoryDescriptor.RepositoryKey; }
    }
}

Create content selector dojo widget

(TopLevelCatalogContentSelector widget defined in above step)

define([
    // dojo
    "dojo/_base/declare",
    "dojo/aspect",
    // epi
    "epi-cms/widget/ContentSelector"
], function (
    // dojo
    declare,
    aspect,
    // epi
    ContentSelector
) {
        return declare([ContentSelector], {
            _getDialog: function () {
                // tags:
                //      protected extensions

                var dialog = this.inherited(arguments);
                if (this.dialog && this.contentSelectorDialog) {
                    this.own(
                        aspect.before(this.contentSelectorDialog.tree.model.store, "query", function (query, queryOptions) {
                            query.toplevel = true;
                        }, true),
                        aspect.around(this.contentSelectorDialog.tree, "selectContent", function (originalMethod) {
                            return function (contentReferenceAsString, setFocus, needParentRefresh, onComplete) {
                                if (this.selectedItem.contentLink === contentReferenceAsString) {
                                    return;
                                }

                                originalMethod.apply(this, arguments);
                            };
                        })
                    );
                }

                return dialog;
            }
        });
    });

Use it in your code

/// <summary>
/// Gets or sets the product content reference.
/// </summary>
/// <value>
/// The product content reference.
/// </value>
[Display(
    Name = "Product/Course Variant",
    Description = "The variant to be added to the basket - will use the variant on the page level by default if empty",
    GroupName = SystemTabNames.Content,
    Order = 10
)]
[UIHint("TopLevelProductVariation")]
[AllowedTypes(typeof(SupplierProductVariant), typeof(CourseScheduleVariant))]
public virtual ContentReference ProductContentReference { get; set; }

Updated code for TopLevelCatalogContentSelector widget

define([
    // dojo
    "dojo/_base/declare",
    "dojo/aspect",
    // epi
    "epi-cms/widget/ContentSelector"
], function (
    // dojo
    declare,
    aspect,
    // epi
    ContentSelector
) {
        return declare([ContentSelector], {
            _getDialog: function () {
                // tags:
                //      protected extensions

                var dialog = this.inherited(arguments);
                if (this.dialog && this.contentSelectorDialog) {
                    this.own(
                        aspect.before(this.contentSelectorDialog.tree.model.store, "query", function (query, queryOptions) {
                            query.toplevel = true;
                        }, true),
                        aspect.around(this.contentSelectorDialog.tree, "selectContent", function (originalMethod) {
                            return function (contentReferenceAsString, setFocus, needParentRefresh, onComplete) {
                                if ((this.selectedItem && this.selectedItem.contentLink) === contentReferenceAsString) {
                                    return;
                                }

                                originalMethod.apply(this, arguments);
                            };
                        })
                    );
                }

                return dialog;
            }
        });
    });