I think it is related to the following code in EnvironmentVariablesNodeLoader:

for (NodeProperty<?> nodeProperty : Hudson.getInstance().getGlobalNodeProperties()) {
    if (nodeProperty instanceof EnvironmentVariablesNodeProperty) {
        EnvironmentVariablesNodeProperty variablesNodeProperty = (EnvironmentVariablesNodeProperty) nodeProperty;
        EnvVars envVars = variablesNodeProperty.getEnvVars();
        EnvInjectEnvVars envInjectEnvVars = new EnvInjectEnvVars(logger);
        configNodeEnvVars.putAll(envVars);
        envInjectEnvVars.resolveVars(configNodeEnvVars, nodeEnvVars);
    }
}

Without the "Prepare jobs environment" checked, the if statement above resolves to false so env vars are not updated.... i think.

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