Keccak subset SHA-3 also contains SHA384 (192 bit) and SHA512 (256 bit), so the Bitcoin Core can be upgraded if the need ever arises. Plus, I am sure more secure algorithms will be developed in the future that Bitcoin can be upgraded to if needed.

That said, I've yet to hear of a single collision with SHA256, and we know that cryptographers and hackers are trying to do it. But if you can produce any SHA256 collisions, please show us all, but I don't think you can.

This all is really a non-issue.