Here is the hack to get around the issue, in case anyone else needs it. In short, to get to the properties of Chart object, one has to create ChartControl first:
#load "packages/FSharp.Charting.0.87/FSharp.Charting.fsx"
open FSharp.Charting
open FSharp.Charting.ChartTypes
open System.Drawing
open System.Windows.Forms
let chart = Chart.Line([0,0;1,0;2,1;3,1;5,0; 6,0])
.WithYAxis(Title = "Y", TitleAlignment = StringAlignment.Far)
.WithXAxis(Title = "x", TitleAlignment = StringAlignment.Far)
let ctrl = new ChartControl(chart, Dock=DockStyle.Fill)
let chartObj = ctrl.Controls |> Seq.cast<Control> |> Seq.pick (function | :? DataVisualization.Charting.Chart as x -> Some x | _-> None)
chartObj.ChartAreas.[0].AxisY.TextOrientation <- DataVisualization.Charting.TextOrientation.Horizontal
let form = new Form(Visible = true, TopMost = true, Width = 700, Height = 500)
form.Controls.Add(ctrl)
form.Show()