A few things:

1. Be careful given that the old indexOf is resilient to undefined arrays.
2. Also, performance characteristics of built-ins isn't always as optimal as one would expect.
3. Do we consider removals from core.ts to be breaks?

For 3), all of core.ts after line 20 is internal.

what is the rational for this change? we do have multiple array/list helper functions that are hand-rolled, like map, filter, foreach, etc.. so what is the guiding principal here?

I think we should be removing any shim function once we move to an ES version that supports it natively. That might include contains (Array.includes), stringContains (String.includes) and find one day.
map and filter both handle undefined, which we use instead of empty arrays to reduce allocations; ideally we would use an immutable emptyArray for that (#16312), and then use builtin map and filter instead.
forEach is ambiguous over 3 different meanings, and should be replaced with a for loop, some, or find.