Won’t IDEA automatically index/execute some Gradle code when possible? As soon as you execute an arbitrary binary/script from the project directory, the isolation of the JVM doesn’t matter.
The alternative is a whitelist approach. Instead of disallowing dangerous features you're enabling only the features you need.
So a build system like Gradle or Maven (same thing really) has a limited set of primitives it is allowing access to. It's not loading, say, the entire JVM and all the Java core libraries and then listing all those you can't use.
You see the difference? If nothing else, the blacklist approach is going to fail when the virtual machine (or whatever) adds a new API call upstream and it's added without intent to the sandbox by simply doing an update where nobody has thought to disable it.
Another way of looking at this is Gradle isn't being compiled into Java bytecode and run in the same environment as the IDE (sandboxed or otherwise). That is inherently riskier.