Actually, every time
@Carlo S calls someone "brother" or calls us all "brothers", I'm getting a mental image of
or rather
:closedeyesmile:
I don't mind, really
Yes, the first time you start the game and all the applied rpy files aren't compiled by Ren'Py yet, there are no corresponding rpyc files for it yet to use. It looks like before it gets those new files compiled, old files from the rpa archive are already loaded into Ren'Py and since they already contain the same definitions for some constants, it throws an error message about these "conflicts". In case of this kind of conflicts Ren'Py should and normally does prefer newer files with the same names to the old ones, but for some unknown reason, not in this case.
On the second run newer rpyc files already exist and Ren'Py will ignore the old ones inside the rpa, as it normally does.
It looks like a bug or design flaw of the Ren'Py engine itself. This thing normally doesn't happen, this game is one of the few I've ever seen it. It could have something to do with the game being larger and having larger script files or a larger number of script files than most games have. Or maybe the whole combination of being larger, having a large number of script files and also having definitions being scattered around into multiple of these files.
I don't know, just guessing.