The pythonnet method resolution (the Bind method found in the methodbinder.cs file) could be improved quite a lot IMHO. Anyway, this method currently doesn't really care about types hierarchies.

One simple solution is to change the MethodSorter class so it favors derived class when it sorts methods to determine which one will be choosen by the Bind call.

Before:

internal class MethodSorter : IComparer
{
    int IComparer.Compare(object m1, object m2)
    {
        int p1 = MethodBinder.GetPrecedence((MethodBase)m1);
        int p2 = MethodBinder.GetPrecedence((MethodBase)m2);
        if (p1 < p2)
        {
            return -1;
        }
        if (p1 > p2)
        {
            return 1;
        }
        return 0;
    }
}

After:

internal class MethodSorter : IComparer
{
    int IComparer.Compare(object m1, object m2)
    {
        var me1 = (MethodBase)m1;
        var me2 = (MethodBase)m2;
        if (me1.DeclaringType != me2.DeclaringType)
        {
            // m2's type derives from m1's type, favor m2
            if (me1.DeclaringType.IsAssignableFrom(me2.DeclaringType))
                return 1;

            // m1's type derives from m2's type, favor m1
            if (me2.DeclaringType.IsAssignableFrom(me1.DeclaringType))
                return -1;
        }

        int p1 = MethodBinder.GetPrecedence((MethodBase)m1);
        int p2 = MethodBinder.GetPrecedence((MethodBase)m2);
        if (p1 < p2)
        {
            return -1;
        }
        if (p1 > p2)
        {
            return 1;
        }
        return 0;
    }
}

Note I've not ran extensive tests, so I'm not sure this will not break something else. As I say this whole method binding code seems fragile.