I didn't look too hard, but I don't see anything about encryption. I know there can be just compiled .rpyc files instead of .rpy readable source code, or files could be in .rpa archive, but neither is encryption and tools exist to deal with both. Even if there's support for actual encryption with unbreakable ciphers, the game itself must still be able to decrypt data to be able to use it, and that's the weak point. If the game can do it, someone else can too, because everything required for it (some decryption key) must be somewhere in game's files.
Encryption might be the wrong term, I was tired when I commented at that point, but there is a way to prevent them from being read normally like a .rpy can be. The tools exist, but that's extra work. We've already seen through comments here how extra work is viewed, no offense to other players, of course. Also, no encryption is truly unbreakable, not even the most sophisticated military grade encryption. The difference is how much time and effort would be needed. In reality, they only seem unbreakable because there's nobody on the planet who has been stubborn enough to try until they succeed, that and it might take longer than the person trying has left to live.
Still think it'd be easy to fix the cheater issue as regardless of what he does inspection of the code would find what he's done. Sure he can obfuscate it, the very basic level of that would be changing the name of the variable. Of course if he really was die hard on stopping you from changing the code he could try certain methods, although as has already been said as long as it's an offline game there's nothing he can really do to stop us.
And if he starts setting backup variables? That's always an option. For example, he could make it so that if a save is loaded into a game with an alteration to make $Cheater = False, I don't have the code in front of me, this is an example only, he could then make $Tamper = True and then set that so that if $Tamper = True, then $Cheater is automatically changed to True as well. $Tamper would be False by default, but it would turn True if it found $Cheater was False when a save was loaded. To prevent this from firing on a false positive because $Cheater is False until the player cheats, he could also add a $Cheated variable that would be set to True if a cheat was used as a backup cheater variable, which would fire at every load cycle. It could become a long string of variables that continually set and reset the cheater flag and this would eventually come down to who is more stubborn, the players or Selebus himself. Given how he never budges against a complaint about his choices in design, like how consequences actually have an impact, which has come up multiple times, I would put money on Selebus winning that battle. Hell, if I was making this game, I would already have at least 10 backups from the start in a chain set up to make sure that flag stays active. If I'm going to put the flag in there, I am going to make sure it gets used since, if there is one thing I dislike in programming, it's keeping useless code.