Technical feedback: itch app detects “notification helper” executable. I’m not sure if there’s an easy way around it (besides just deleting that file) though since game engines just export things this way.
I found that game manifest can be used to indicate a canonical exe to launch (https://itch.io/docs/itch/integrating/manifest.html). It’s apparently preferred to change directory structure but if game engine exports it this way, not much choice.