How do I configure other user defined data-type with Entity Framework Core?

I've found a workaround.

At the and of the OnModelCreating method I'll just remove the generated ColumnType annotation:

  modelBuilder
    .Entity(typeof(MyEntity))
    .Property(nameof(MyEntity.Status))
    .Metadata
    .RemoveAnnotation("Relational:ColumnType");

A small helper function that goes over all entities and removes that annotation automatically from all properties that have it should be enough for now.

public static class ModelBuilderExtensions
{
    public static ModelBuilder RemoveAnnotations<TDbContext>(this ModelBuilder modelBuilder, TDbContext context, string name, IList<string> values) where TDbContext : DbContext
    {
        var bindingFlags = 
            BindingFlags.Instance | 
            BindingFlags.Public | 
            BindingFlags.DeclaredOnly;

        var entityMethod =
            typeof(ModelBuilder)
                .GetMethods()
                .Single(m =>
                    m.Name == nameof(ModelBuilder.Entity) &&
                    m.GetGenericArguments().Length == 1 &&
                    m.GetParameters().Length == 0
                )
                .GetGenericMethodDefinition();

        foreach (var contextProperty in typeof(TDbContext).GetProperties(bindingFlags))
        {
            var entity =
                contextProperty
                    .PropertyType
                    .GetGenericArguments()
                    .SingleOrDefault();

            if (entity is null)
            {
                continue;
            }

            // Only the generic overload returns properties. The non-generic one didn't work.
            var generitcEntityMethod = entityMethod.MakeGenericMethod(entity);

            foreach (var property in entity.GetProperties(bindingFlags))
            {
                var entityTypeBuilder = (EntityTypeBuilder)generitcEntityMethod.Invoke(modelBuilder, null);

                if (entityTypeBuilder.Metadata.FindProperty(property) is null)
                {
                    continue;
                }

                var annotation = 
                    entityTypeBuilder
                        .Property(property.Name)
                        .Metadata
                        .FindAnnotation(name);

                if (values.Contains(annotation?.Value))
                {
                    entityTypeBuilder
                        .Property(property.Name)
                        .Metadata
                        .RemoveAnnotation(name);
                }
            }
        }
        return modelBuilder;
    }
}

Usage:

modelBuilder.RemoveAnnotations(this, "Relational:ColumnType", new[] { "Enumeration" });