Try adding second generic type parameter to your second method:
Public Function DoSomething2(Of T1 As {Parent}, T2 As {CustomList2(Of T1), New})() As T2
Dim instance As New T2
'This method would work if I could call this method
instance.MyCustomList2Method()
Return instance
End Function
When it looks like that, you can call it like this:
Me.DoSomething2(Of Child, CustomList2(Of Child))()