If you connect a full node to the bitcoin network you also download data from random strangers. As I understand it the data in this file is subjected to exactly the same checks as data downloaded by the bitcoin client itself. Should the data be misformatted it will be rejected. If some of the end blocks got reorganized the client will sort it out once it connects to the network proper.

Of course you are right to be paranoid but I don't see the need for this torrent to align with checkpoints in the code itself.