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It might be something strange with permissions for your Godot project files. Try this: click the Windows button in the lower left of the screen, type "command" so you see "Command Prompt", right click "Command Prompt" and choose "Run as Administrator". That opens Command Prompt and then try to run the script again.
If that doesn't work, you can go to your Godot project folder, right click, Properties, Security tab, advanced, check "Replace all child object permissions...", then click "Add", "Select a principal", type your Windows user name, click Check Names, then OK, check "Full Control", OK again, OK one more time, I lied there's another OK
done! That will change all the permissions of your Godot project files so your Windows user has full control. Whew.
Many thanks to you and Mario for all your help, I have done the 2 options with the same result. As far as I read here:
It could because of python-windows issue.
But I think I'd better stick with the first method: replace it manually. For the project I'm doing, there aren't that many Spine nodes that need to be replaced, so it's not a tedious job. It is also an option until Godot 4 arrives, which will be soon. Once again, thank you very much for your help. I will make a video tutorial with my experience with the first method to help people who want to update the runtime.