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Yes, the fact that we can mutate lists with anything is super scary: Here is a basic example.
On one hand, this is definitely a gap, on the other hand, you are very unlikely to run into it in practice.
The whole “pass an array/object into some function that will mutate it for you” pattern is not very popular in JS , you are much more likely to encounter code that just gives you a new array as a return value and treats its arguments as read-only.
If you validate your data at the boundaries where it enters your system (e.g. incoming JSON from HTTP responses), TypeScript is plenty good enough for almost all practical uses.