[anfilt]

The bitstream is probably decrypted as it enters the chip. After that at best you might have some simple xoring at each CLB to make someone probing with needles life harder.

Also making sure each data line is not on the top or bottom layer to make non-destructive access harder. At which point you going to need careful application of acid or focused ion beam ablation.

[trollied]

The encryption has been broken. You can read about it here https://news.ycombinator.com/item?id=22915831

[anfilt]

I was not saying anything about that, but if you look at that paper or video you can see the bitstream is passed through an AES decryption stage before programing the logic fabric. This break found a way to read the data after that AES stage.

However, I was just explaining how encryption generally works for these things. Weather or not breaks exist for some chips.