Scene variables GameObject disappears from hierarchy after saving and reloading scene

Steps to Repro:
# Create a new Project
# Create a New Scene and click to open it
# Project window > Right-click > Create > Visual Scripting > Script Graph
# Observe Scene variables GameObject in the hierarchy
# Save Scene
# Project > Double Click on Scene to reopen it

Actual Result:
Scene variables GameObject disappears from the hierarchy

Expected Result:
Scene variables GameObject remains in the hierarchy

Reproducible on: 2021.2.0a6, 2021.1.0b1, 2021.1.0b1

Note: Visual Scripting was introduced in 2021.1.0b1

Package Version 1.5.1-pre.5

Environment:
Windows 10, Mac 10.15