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Previously any user could modify these certs directly, even on vanilla OS images from Google themselves, without installing Magisk or any tools at all, just by writing to disk. Right now, that's widely used and included in the setup guides for lots & lots of tools. All of that will start breaking for users when Android 14 arrives.
I totally agree it is possible to work around this restriction, but it's going to be significantly more complicated, and those changes will only be required because the OS used to let you read & write these files all by yourself, and now it doesn't.
I don't think Android should move further in a direction where it's impossible to directly control anything unless you install a 3rd party modification to the root daemon. That's not a good result. These are important settings and the OS itself should allow you to control them (behind reasonable safeguards & warnings, but still).
Wait, what tools, and why would they need you to modify existing certificates? That's super sketchy.
This is modifying system CA certs on your own device, with root access. There's plenty of examples in the article, but most commonly you'd want to add your own CAs so that you can intercept and inspect your own network traffic. There's a wide world of developer/researcher/reverse engineering tools that do exactly that, there's a demo here: https://httptoolkit.com/android/
It could plausibly be malicious, but it requires direct root access on the device, and if somebody has root access there's already far more malicious options available to them so it's not a meaningful threat in any sense.