And if the text file is ever the weak point there's always some form of.encryption and hashing to act as a bit of a halfway house between completely open and reasonably secure.
Which you could make more or less complicated (and assuming the are converted back to text on file load, then decryption can just be bypassed to allow home/development files). I'm not sure how you'd set it up for best security and usability.
I'm not sure about secret 'run time' data, encrypting the data stream is easy but at some point it has to be read by software that the user has access to. And even if you try to tie it into the program, I think anything you do, you could also fake. Even if you encrypt today's object positions with the last frame data (which itself requires you to be inflexible about timings and the like), that just means you need to draw that as well as the transparent walls version.