VFX Graph prefabs are not fully instanced when they are instantiated via a script

Steps to reproduce:
1. Open the attached “VFXBugReport.zip“ project (link in the internal comments)
2. Open the “SampleScene”
3. Select the “Root_Copy_Pasted” GameObject in the Hierarchy and disable it in the Inspector
4. Select the “Root_Instantiated” GameObject in the Hierarchy and enable it in the Inspector
5. Open the Frame Debugger window (Window > Analysis > Frame Debugger)
6. Press the “Enable” button while the VFX Graph is playing in the Game view
7. Observe the number of “RenderLoop.Draw” calls

Actual result: There are 15 draw calls (1 for almost every prefab instance of both VFX Graph assets)
Expected result: There are 2 draw calls (draw calls are instanced to 2 because there are only 2 unique VFX Graph assets used)

Reproducible with: 6000.0.67f1, 6000.3.7f1, 6000.4.0b7, 6000.5.0a6

Reproducible on: Windows 11 Pro (25H2)
Not reproducible on: No other environment tested

Notes:

• To observe the Expected result, disable the “Root_Instantiated” GameObject and enable the “Root_Copy_Pasted” GameObject
• The number of draw calls in the Actual result is different for each project but the same project always produces the same number of draw calls
• The prefabs need to be instantiated from at least 2 different VFX Graph assets for the instancing to break
• Reproducible with URP and HDRP (VFX Graph not supported in Built-in RP)
• Reproducible in a new project
• Reproducible in the Player