standalone_vm_runner: configs are still a json file

[nagisa]

In https://github.com/near/nearcore/pull/6693 we replaced json configs with flat differential configs instead. However this only applies to the versioned configs consumed by nearcore. Tools like near-vm-runner-standalone appear continue expecting a full json file for a config, which is now much harder to specify given that there isn't a template file to use any longer.

Tools like near-vm-runner-standalone should be ported to use the flat-differential config file format as well.