If anyone else has this issue, then please know that my solution was to create a new model for Konstrukt (in my case):

// Must be a super class of Resource for the ReplaceVisitor to work
public class ResourceModel : Resource
{
    public readonly Resource Resource;

    public ResourceModel (Resource resource)
    {
        // Copy properties
        Id = resource.Id;
        Name = resource.Name;
    }

    // a new property that then allows for setting
    public new ICollection<ResourceType> ResourceTypes {
        get => Resource.ResourceTypes;
        set => UpdateCollectionContents(Resource.ResourceTypes, value);
    }

    public static void UpdateCollectionContents<TEntity> (ICollection<TEntity> collection, IEnumerable<TEntity> newContents)
    {
        collection.Clear();
        foreach (var entity in newContents)
        {
            collection.Add(entity);
        }
    }
}

However that then requires that you have a custom repository (which I already did). Unfortunately all the Expressions for where and order by are then refer to your new model rather than your entity. So you need to do some magic to change the input type of your expression:

public static Expression<Func<Resource, TResult>> ToEntityExpression<TResult> (Expression<Func<ResourceModel, TResult>> expression)
{
    var resourceParam = Expression.Parameter(typeof(Resource));
    return Expression.Lambda<Func<Resource, TResult>>(
        new ReplaceVisitor(expression.Parameters[0], resourceParam).Visit(expression.Body)!,
        resourceParam);
}


internal class ReplaceVisitor : ExpressionVisitor
{
    private readonly Expression _from, _to;
    public ReplaceVisitor (Expression from, Expression to)
    {
        this._from = from;
        this._to = to;
    }
    public override Expression? Visit (Expression? node)
    {
        return node == _from ? _to : base.Visit(node);
    }
}