yes - expect there to be differences. For instance they will add new features such as profiles, or in your case they have modified the bot defense signatures. This is expected. If you want to check your config then maybe start with a known quantity such as the number of virtual servers, number of pools, nodes etc
Aside from this I would imagine differences will exist because of updates to signatures or even the way a command might change from code version to code version. To me it seems like it has switched from plaintext to some sort of hashed value instead.