How is the source code there? One renpy is and has been open source since it's start and secondly We have packed the images , the videos , music , core systems pretty tightly until or unless you unren it via bat.
Rpyc files get created regardless and deleting them or deleting persistent in renpy does nothing except remove save data , what happened with you is you created an rpyc file when you first launched with error codes , as I said before no one else had this issue here.
There's no definition here neither is it sloppy , that's like saying leaving repositories in any game's folder is "sloppy"
Every game and I mean normal or Triple AAA games has most of it's files in it's main directory folder , no one packs all the files because it takes more time to then unpack and read it by engine , which becomes a problem if you don't have a beast gaming rig or something.
Example of this case in Resident evil 4's root folder
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Uncharted 4 -
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You might want to educate yourself on how games and code actually work before teaching other devs about their own , regardless hope you enjoy the game mate.