yes it's on purpose! since there's so much overlap in assets between seasons, excluding some can get complicated and lead to bugs, so we decided it'd be safer to include the same assets in each build of the game! :)
Viewing post in Cool Kid Cody: Season 2 comments
"Looking closer, the files actually do differ. (by just 2kb!) That is quite confusing when they both share a filename... Still I am relieved to know that there has been no mistake and the files do contain S1 & S2 respectively and seperately, as I suspected but could not confirm without playing." - Patches
"Also, as a linux gamer who has a distaste for any form of DRM and hardly ever uses services such as Steam, I appreciate you still offering the itch.io releases, even if they seem to be an afterthought when compared to the Steam release. (Including Steam keys with the purchase was also a nice touch I hadn't expected, yet appreciate nonetheless.)" - Patches