Is it possible to change max_input_vars in runtime?
No, it's not possible to change it at runtime.
This is because at runtime the input has been already processed.
So the setting either resulted in an error already or it is too late to change it.
This is also documented in the manual as it lists places where you can change ini directives:
If you're unsure where all those places to change PHP configuration are and how to use them, there is another page in that section: