I'm not in any way related to the developer so I can't know for sure if it is a false positive or not, but I can argue in favor of the developer because you tested the AlteredVersion03Installer.exe and an installer usually needs more permissions than a normal .exe for it to install the game, possibly triggering that as a false positive. The exe inside AlteredVersion03.zip doesn't trigger anything on VirusTotal you can check it yourself. In any case I'd recommend you running any Itch.io games on something like SandboxiePlus or any sandboxing software if you're worried about viruses. It's good practice.
VirusTotal result for the installer:https://www.virustotal.com/gui/file/90537c93549f7f6f9c1ec81751a530a7b1ac4f1334e1...
VirusTotal result for the exe inside the game's folder:https://www.virustotal.com/gui/file/a62c46f7fa2652a78c091a9b4eda7111f80b75701470...