Interesting tip, as I do not use compressed files (often quality loss).
It didn't cross my mind to ask ..
Now that scripts are altered in the process (I didn't know) is this common or was it something different when compressing the file of this game?
Can it serve as a rule when this problem happens?
I'm not familiar with compressing images but I have used a lot of compressed versions before and this is the first time something like this has happened. This seems to be result of combination of reasons.
This game has been designed so that incest patching would be as easy as possible. Therefore all information you'd like to alter to your liking is easily accessible in their own separate file, in this case 'game/names.rpa'. With this game incest patching means simply editing and/or replacing that file. There are many different ways to implement such feature.
Stuff like scripts and images are usually packed together. To be able to alter or compress images and other files, you need to "unren" the package so you can access them outside of the game. When scripts and images are unpacked they are put in their own directories, either automatically or manually to keep things tidy. As a result, scripts ended up in 'game/scripts'.
For some reason, "names.rpa" in original got converted to "names.rpy". I assume this is because of unren. I've seen something similar before and fixing it was as simple as renaming the file extension. This is NOT advisable though but I thought I'd give it a shot. It worked then but it didn't work now. Quick glance inside the files revealed there were differences, .rpa was almost three times the size of .rpy and contained some code that was tidied away from .rpy, again probably due to unren.
As a result, 'game/names.rpa' changed into 'game/scripts/names.rpy' and because both file and path have changed, incest patching is slightly different between original and compressed versions.